#はじめに
仕事でGoogleDriveにあるPDFを一つにまとめる必要があったので探したら出てきたので少し加工して使わせて頂きました。
注意点としては、パスワードでロックされてたらエラーになります。(当たり前か)

##ソースコード
ベースになっているソースコードは、こちらのstack overflowの中にChrome V8搭載のランタイムで動くのもあったので、マージするPDFを配列で渡せるようにだけ書き換えます。

こういう感じのコードになります。

code.gs

/**
 * Original code by pokyCoder, retrieved from https://script.google.com/d/1X85wgpK71UWpmAVpeDOXbv84WQyaAZuf8WTjO-5MKxmWT716Tw5G1K1L/edit?usp=sharing
 * Edited to work in V8  (Apr 16, 2020)
 * References:
 * - https://issuetracker.google.com/issues/36753526
 * - https://stackoverflow.com/questions/15414077/merge-multiple-pdfs-into-one-pdf
 * Original Notes:
 *
 * Merges all given PDF files into one.
 *
 * @param {Folder} directory the folder to store the output file
 * @param {string} name the desired name of the output file
 * @param {Array of File} PDFオブジェクトファイルの配列。要素0が表紙になる。
 * @return {File} the merged file
 */


function mergePdfs(directory, name, pdf_list) {
//function mergePdfs(directory, name, pdf1, pdf2, opt_pdf3) {  //引数をファイルオブジェクトの配列に変更
  
  if (name.slice(-4) != '.pdf') {
    
    name = name + '.pdf';
    
  }
  var newObjects = ['1 0 obj\r\n<</Type/Catalog/Pages 2 0 R >>\r\nendobj'];
  var pageAddresses = [];
  
  for (var argumentIndex in pdf_list) {
  //for (var argumentIndex = 2; argumentIndex < arguments.length; argumentIndex++) {  //引数に合わせて変更した。
  
    var bytes = pdf_list[argumentIndex].getBlob().getBytes();
    //var bytes = arguments[argumentIndex].getBlob().getBytes();  //リスト名を変更。

    var xrefByteOffset = '';
    var byteIndex = bytes.length - 1;
    while (!/\sstartxref\s/.test(xrefByteOffset)) {
      
      xrefByteOffset = String.fromCharCode(bytes[byteIndex]) + xrefByteOffset;
      byteIndex--;
      
    }
    xrefByteOffset = +(/\s\d+\s/.exec(xrefByteOffset)[0]);
    var objectByteOffsets = [];
    var trailerDictionary = '';
    var rootAddress = '';
    do {
      
      var xrefTable = '';
      var trailerEndByteOffset = byteIndex;
      byteIndex = xrefByteOffset;
      for (byteIndex; byteIndex <= trailerEndByteOffset; byteIndex++) {
        
        xrefTable = xrefTable + String.fromCharCode(bytes[byteIndex]);
        
      }
      xrefTable = xrefTable.split(/\s*trailer\s*/);
      trailerDictionary = xrefTable[1];
      if (objectByteOffsets.length < 1) {
        
        rootAddress = /\d+\s+\d+\s+R/.exec(/\/Root\s*\d+\s+\d+\s+R/.exec(trailerDictionary)[0])[0].replace('R', 'obj');
        
      }
      xrefTable = xrefTable[0].split('\n');
      xrefTable.shift();
      while (xrefTable.length > 0) {
        
        var xrefSectionHeader = xrefTable.shift().split(/\s+/);
        var objectNumber = +xrefSectionHeader[0];
        var numberObjects = +xrefSectionHeader[1];
        for (var entryIndex = 0; entryIndex < numberObjects; entryIndex++) {
          
          var entry = xrefTable.shift().split(/\s+/);
          objectByteOffsets.push([[objectNumber, +entry[1], 'obj'], +entry[0]]);
          objectNumber++;
          
        }
        
      }
      if (/\s*\/Prev/.test(trailerDictionary)) {
        
        xrefByteOffset = +(/\s*\d+\s/.exec(/\s*\/Prev\s*\d+\s/.exec(trailerDictionary)[0])[0]);
        
      }
      
    } while (/\s*\/Prev/.test(trailerDictionary));
    var rootObject = getObject(rootAddress, objectByteOffsets, bytes);
    var pagesAddress = /\d+\s+\d+\s+R/.exec(/\/Pages\s*\d+\s+\d+\s+R/.exec(rootObject)[0])[0].replace('R', 'obj');
    var pagesObject = getObject(pagesAddress, objectByteOffsets, bytes);
    var objects = getDependencies(pagesObject, objectByteOffsets, bytes);
    var newObjectsInsertionIndex = newObjects.length;
    for (var objectIndex = 0; objectIndex < objects.length; objectIndex++) {
      
      var newObjectAddress = [(newObjects.length + 3) + '', 0 + '', 'obj'];
      if (!Array.isArray(objects[objectIndex])) {
        
        objects[objectIndex] = [objects[objectIndex]];
          
      }
      objects[objectIndex].unshift(newObjectAddress);
      var objectAddress = objects[objectIndex][1].match(/\d+\s+\d+\s+obj/)[0].split(/\s+/);
      objects[objectIndex].splice(1, 0, objectAddress);
      if (/\/Type\s*\/Page[^s]/.test(objects[objectIndex][2])) {
        
        objects[objectIndex][2] = objects[objectIndex][2].replace(/\/Parent\s*\d+\s+\d+\s+R/.exec(objects[objectIndex][2])[0], '/Parent 2 0 R');
        pageAddresses.push(newObjectAddress.join(' ').replace('obj', 'R'));
        
      }
      var addressRegExp = new RegExp(objectAddress[0] + '\\s+' + objectAddress[1] + '\\s+' + 'obj');
      objects[objectIndex][2] = objects[objectIndex][2].replace(addressRegExp.exec(objects[objectIndex][2])[0], newObjectAddress.join(' '));
      newObjects.push(objects[objectIndex]);
      
    }
    for (var referencingObjectIndex = newObjectsInsertionIndex; referencingObjectIndex < newObjects.length; referencingObjectIndex++) {
      
      var references = newObjects[referencingObjectIndex][2].match(/\d+\s+\d+\s+R/g);
      if (references != null) {
        
        var string = newObjects[referencingObjectIndex][2];
        var referenceIndices = [];
        var currentIndex = 0;
        for (var referenceIndex = 0; referenceIndex < references.length; referenceIndex++) {
          
          referenceIndices.push([]);
          referenceIndices[referenceIndex].push(string.slice(currentIndex).indexOf(references[referenceIndex]) + currentIndex);
          referenceIndices[referenceIndex].push(references[referenceIndex].length);
          currentIndex += string.slice(currentIndex).indexOf(references[referenceIndex]);
          
        }
        for (var referenceIndex = 0; referenceIndex < references.length; referenceIndex++) {
          
          var objectAddress = references[referenceIndex].replace('R', 'obj').split(/\s+/);
          for (var objectIndex = newObjectsInsertionIndex; objectIndex < newObjects.length; objectIndex++) {
            
            if (arrayEquals(objectAddress, newObjects[objectIndex][1])) {
              
              var length = string.length;
              newObjects[referencingObjectIndex][2] = string.slice(0, referenceIndices[referenceIndex][0]) + newObjects[objectIndex][0].join(' ').replace('obj', 'R') +
                string.slice(referenceIndices[referenceIndex][0] + referenceIndices[referenceIndex][1]);
              string = newObjects[referencingObjectIndex][2];
              var newLength = string.length;
              if (!(length == newLength)) {
                
                for (var subsequentReferenceIndex = referenceIndex + 1; subsequentReferenceIndex < references.length; subsequentReferenceIndex++) {
                  
                  referenceIndices[subsequentReferenceIndex][0] += (newLength - length);
                  
                }
                
              }
              break;
              
            }
            
          }
          
        }
        
      }
      
    }
    for (var objectIndex = newObjectsInsertionIndex; objectIndex < newObjects.length; objectIndex++) {
      
      if (Array.isArray(newObjects[objectIndex])) {
        
        if (newObjects[objectIndex][3] != undefined) {
          
          newObjects[objectIndex] = newObjects[objectIndex].slice(2);
          
        } else {
          
          newObjects[objectIndex] = newObjects[objectIndex][2];
          
        }
        
      }
      
    }
    
  }
  newObjects.splice(1, 0, '2 0 obj\r\n<</Type/Pages/Count ' + pageAddresses.length + ' /Kids [' + pageAddresses.join(' ') + ' ]>>\r\nendobj');
  newObjects.splice(2, 0, '3 0 obj\r\n<</Title (' + name + ') /Producer (PdfManipulation.mergePdfs\\(\\), a Google Apps Script project by Jarom Luker \\(pricebook@hbboys.com\\)) /CreationDate (D' +
       Utilities.formatDate(new Date(), CalendarApp.getDefaultCalendar().getTimeZone(), 'yyyyMMddHHmmssZ').slice(0, -2) + "'00) /ModDate (D" + Utilities.formatDate(new Date(),
       CalendarApp.getDefaultCalendar().getTimeZone(), 'yyyyMMddHHmmssZ').slice(0, -2) + "'00)>>\r\nendobj");
  var byteOffsets = [0];
  var bytes = [];
  var header = '%PDF-1.3\r\n';
  for (var headerIndex = 0; headerIndex < header.length; headerIndex++) {
    
    bytes.push(header.charCodeAt(headerIndex));
    
  }
  bytes.push('%'.charCodeAt(0));
  for (var characterCode = -127; characterCode < -123; characterCode++) {
    
    bytes.push(characterCode);
    
  }
  bytes.push('\r'.charCodeAt(0));
  bytes.push('\n'.charCodeAt(0));
  while (newObjects.length > 0) {
    
    byteOffsets.push(bytes.length);
    var object = newObjects.shift();
    if (Array.isArray(object)) {
      
      var streamKeyword = /stream\s*\n/.exec(object[0])[0];
      if (streamKeyword.indexOf('\n\n') > streamKeyword.length - 3) {
        
        streamKeyword = streamKeyword.slice(0, -1);
        
      } else if (streamKeyword.indexOf('\r\n\r\n') > streamKeyword.length - 5) {
        
        streamKeyword = streamKeyword.slice(0, -2);
        
      }
      var streamIndex = object[0].indexOf(streamKeyword) + streamKeyword.length;
      for (var objectIndex = 0; objectIndex < streamIndex; objectIndex++) {
        
        bytes.push(object[0].charCodeAt(objectIndex))
        
      }
      bytes = bytes.concat(object[1]);
      for (var objectIndex = streamIndex; objectIndex < object[0].length; objectIndex++) {
        
        bytes.push(object[0].charCodeAt(objectIndex));
        
      }
      
    } else {
      
      for (var objectIndex = 0; objectIndex < object.length; objectIndex++) {
        
        bytes.push(object.charCodeAt(objectIndex));
        
      }
      
    }
    bytes.push('\r'.charCodeAt(0));
    bytes.push('\n'.charCodeAt(0));
    
  }
  var xrefByteOffset = bytes.length;
  var xrefHeader = 'xref\r\n';
  for (var xrefHeaderIndex = 0; xrefHeaderIndex < xrefHeader.length; xrefHeaderIndex++) {
    
    bytes.push(xrefHeader.charCodeAt(xrefHeaderIndex));
    
  }
  var xrefSectionHeader = '0 ' + byteOffsets.length + '\r\n';
  for (var xrefSectionHeaderIndex = 0; xrefSectionHeaderIndex < xrefSectionHeader.length; xrefSectionHeaderIndex++) {
    
    bytes.push(xrefSectionHeader.charCodeAt(xrefSectionHeaderIndex));
    
  }
  for (var byteOffsetIndex = 0; byteOffsetIndex < byteOffsets.length; byteOffsetIndex++) {
    
    for (var byteOffsetStringIndex = 0; byteOffsetStringIndex < 10; byteOffsetStringIndex++) {
      
      bytes.push(Utilities.formatString('%010d', byteOffsets[byteOffsetIndex]).charCodeAt(byteOffsetStringIndex));
      
    }
    bytes.push(' '.charCodeAt(0));
    if (byteOffsetIndex == 0) {
      
      for (var generationStringIndex = 0; generationStringIndex < 5; generationStringIndex++) {
        
        bytes.push('65535'.charCodeAt(generationStringIndex));
        
      }
      for (var keywordIndex = 0; keywordIndex < 2; keywordIndex++) {
        
        bytes.push(' f'.charCodeAt(keywordIndex));
        
      }
      
    } else {
      
      for (var generationStringIndex = 0; generationStringIndex < 5; generationStringIndex++) {
        
        bytes.push('0'.charCodeAt(0));
        
      }
      for (var keywordIndex = 0; keywordIndex < 2; keywordIndex++) {
        
        bytes.push(' n'.charCodeAt(keywordIndex));
        
      }
    
    }
    bytes.push('\r'.charCodeAt(0));
    bytes.push('\n'.charCodeAt(0));
    
  }
  for (var trailerHeaderIndex = 0; trailerHeaderIndex < 9; trailerHeaderIndex++) {
    
    bytes.push('trailer\r\n'.charCodeAt(trailerHeaderIndex));
    
  }
  var idBytes = Utilities.computeDigest(Utilities.DigestAlgorithm.MD5, (new Date).toString());
  var id = '';
  for (var idByteIndex = 0; idByteIndex < idBytes.length; idByteIndex++) {
    
    id = id + ('0' + (idBytes[idByteIndex] & 0xFF).toString(16)).slice(-2);
    
  }
  var trailer = '<</Size ' + (byteOffsets.length) + ' /Root 1 0 R /Info 2 0 R /ID [<' + id + '> <' + id + '>]>>\r\nstartxref\r\n' + xrefByteOffset + '\r\n%%EOF';
  for (var trailerIndex = 0; trailerIndex < trailer.length; trailerIndex++) {
    
    bytes.push(trailer.charCodeAt(trailerIndex));
    
  }
  return directory.createFile(Utilities.newBlob(bytes, 'application/pdf', name));
  function getObject(objectAddress, objectByteOffsets, bytes) {
    
    objectAddress = objectAddress.split(/\s+/);
    for (var addressIndex = 0; addressIndex < 2; addressIndex++) {
      
      objectAddress[addressIndex] = +objectAddress[addressIndex];
      
    }
    var object = [];
    var byteIndex = 0;
    for (var key in objectByteOffsets) {
      offset = objectByteOffsets[key]
      
      if (arrayEquals(objectAddress, offset[0])) {
        
        byteIndex = offset[1];
        break;
        
      }
      
    }
    object.push('');
    while (object[0].indexOf('endobj') <= -1) {
      
      if (/stream\s*\n/.test(object[0])) {
        
        var streamLength;
        var lengthFinder = object[0].slice(object[0].indexOf(/\/Length/.exec(object[0])[0]));
        if (/\/Length\s*\d+\s+\d+\s+R/.test(lengthFinder)) {
          
          var lengthObjectAddress = /\d+\s+\d+\s+R/.exec(/\/Length\s*\d+\s+\d+\s+R/.exec(lengthFinder)[0])[0].split(/\s+/);
          lengthObjectAddress[2] = 'obj';
          for (var addressIndex = 0; addressIndex < 2; addressIndex++) {
            
            lengthObjectAddress[addressIndex] = +lengthObjectAddress[addressIndex];
            
          }
          var lengthObject = ''
          var lengthByteIndex = 0;
    for (var key in objectByteOffsets) {
      offset = objectByteOffsets[key]
            
            if (arrayEquals(lengthObjectAddress, offset[0])) {
              
              lengthByteIndex = offset[1];
              break;
              
            }
            
          }
          while (lengthObject.indexOf('endobj') <= -1) {
            
            lengthObject = lengthObject + String.fromCharCode(bytes[lengthByteIndex]);
            lengthByteIndex++;
            
          }
          streamLength = +(lengthObject.match(/obj\s*\n\s*\d+\s*\n\s*endobj/)[0].match(/\d+/)[0]);
          
        } else {
          
          streamLength = +(/\d+/.exec(lengthFinder)[0]);
          
        }
        var streamBytes = bytes.slice(byteIndex, byteIndex + streamLength);
        object.push(streamBytes);
        byteIndex += streamLength;
        while (object[0].indexOf('endobj') <= -1) {
          
          object[0] = object[0] + String.fromCharCode(bytes[byteIndex]);
          byteIndex++;
          
        }
        return object;
        
      }
      object[0] = object[0] + String.fromCharCode(bytes[byteIndex]);
      byteIndex++;
      
    }
    return object[0];
    
  }
  function arrayEquals(array1, array2) {
    
    if (array1 == array2) {
      
      return true;
      
    }
    if (array1 == null && array2 == null) {
      
      return true;
      
    } else if (array1 == null || array2 == null) {
      
      return false;
      
    }
    if (array1.length != array2.length) {
      
      return false;
      
    }
    for (var index = 0; index < array1.length; index++) {
      
      if (Array.isArray(array1[index])) {
        
        if (!arrayEquals(array1[index], array2[index])) {
          
          return false;
          
        }
        continue;
        
      }
      if (array1[index] != array2[index]) {
        
        return false;
        
      }
      
    }
    return true;
    
  }
  function getDependencies(objectString, objectByteOffsets, bytes) {
    
    var dependencies = [];
    var references = objectString.match(/\d+\s+\d+\s+R/g);
    if (references != null) {
      
      while (references.length > 0) {
        
        if (/\/Parent/.test(objectString.slice(objectString.indexOf(references[0]) - 8, objectString.indexOf(references[0])))) {
          
          references.shift();
          continue;
          
        }
        var dependency = getObject(references.shift().replace('R', 'obj'), objectByteOffsets, bytes);
        var dependencyExists = false;
        for (var key in dependencies) {
          entry = dependencies[key]
          
          dependencyExists = (arrayEquals(dependency, entry)) ? true : dependencyExists;
          
        }
        if (!dependencyExists) {
          
          dependencies.push(dependency);
          
        }
        if (Array.isArray(dependency)) {
          
          dependencies = dependencies.concat(getDependencies(dependency[0], objectByteOffsets, bytes));
          
        } else {
          
          dependencies = dependencies.concat(getDependencies(dependency, objectByteOffsets, bytes));
          
        }
        
      }
      
    }
    return dependencies;
    
  }
  
}
/*
 * Splits a PDF file and returns the requested pages.
 *
 * @param {File} pdf the file to split
 * @param {string} pageRange1 a range of pages to include, e.g., '2-4'
 * @param {string} opt_pageRange2 another range of pages to include; add as many as you like
 *
 * return {File} the requested pages in a new file
 */
function splitPdf(pdf, pageRange1, opt_pageRange2) {
  
  var bytes = pdf.getBlob().getBytes();
  var name = pdf.getBlob().getName();
  var xrefByteOffset = '';
  var byteIndex = bytes.length - 1;
  while (!/\sstartxref\s/.test(xrefByteOffset)) {
    
    xrefByteOffset = String.fromCharCode(bytes[byteIndex]) + xrefByteOffset;
    byteIndex--;
    
  }
  xrefByteOffset = +(/\s\d+\s/.exec(xrefByteOffset)[0]);
  var objectByteOffsets = [];
  var trailerDictionary = '';
  var rootAddress = '';
  do {
    
    var xrefTable = '';
    var trailerEndByteOffset = byteIndex;
    byteIndex = xrefByteOffset;
    for (byteIndex; byteIndex <= trailerEndByteOffset; byteIndex++) {
      
      xrefTable = xrefTable + String.fromCharCode(bytes[byteIndex]);
      
    }
    xrefTable = xrefTable.split(/\s*trailer\s*/);
    trailerDictionary = xrefTable[1];
    if (objectByteOffsets.length < 1) {
      
      rootAddress = /\d+\s+\d+\s+R/.exec(/\/Root\s*\d+\s+\d+\s+R/.exec(trailerDictionary)[0])[0].replace('R', 'obj');
      
    }
    xrefTable = xrefTable[0].split('\n');
    xrefTable.shift();
    while (xrefTable.length > 0) {
      
      var xrefSectionHeader = xrefTable.shift().split(/\s+/);
      var objectNumber = +xrefSectionHeader[0];
      var numberObjects = +xrefSectionHeader[1];
      for (var entryIndex = 0; entryIndex < numberObjects; entryIndex++) {
        
        var entry = xrefTable.shift().split(/\s+/);
        objectByteOffsets.push([[objectNumber, +entry[1], 'obj'], +entry[0]]);
        objectNumber++;
        
      }
      
    }
    if (/\s*\/Prev/.test(trailerDictionary)) {
      
      xrefByteOffset = +(/\s*\d+\s*/.exec(/\s*\/Prev\s*\d+\s*/.exec(trailerDictionary)[0])[0]);
      
    }
    
  } while (/\s*\/Prev/.test(trailerDictionary));
  var rootObject = getObject(rootAddress, objectByteOffsets, bytes);
  var pagesAddress = /\d+\s+\d+\s+R/.exec(/\/Pages\s*\d+\s+\d+\s+R/.exec(rootObject)[0])[0].replace('R', 'obj');
  var pagesObject = getObject(pagesAddress, objectByteOffsets, bytes);
  var pagesString = pagesObject.slice(pagesObject.indexOf(/\/Kids\s*\[/.exec(pagesObject)[0]));
  pagesString = pagesString.slice(pagesString.indexOf('[') + 1, pagesString.indexOf(']'));
  var pageAddresses = [];
  while (/\d+\s+\d+\s+R/.test(pagesString)) {
    
    var pageAddress = /\d+\s+\d+\s+R/.exec(pagesString)[0];
    pageAddresses.push(pageAddress.replace('R', 'obj'));
    pagesString = pagesString.slice(pageAddress.length + 1);
    
  }
  var newObjects = ['1 0 obj\r\n<</Type/Catalog/Pages 2 0 R >>\r\nendobj'];
  var objects = [];
  for (var argumentIndex = 1; argumentIndex < arguments.length; argumentIndex++) {
    
    var range = arguments[argumentIndex];
    if (range.indexOf('-') > -1) {
      
      var begin = +range.slice(0, range.indexOf('-'));
      var end = range.slice(range.indexOf('-') + 1, range.length);
      if (end == 'end') {

        for (var pageNumber = begin; pageNumber <= pageAddresses.length; pageNumber++) {
          
          var pageAddress = pageAddresses[pageNumber - 1];
          var page = getObject(pageAddress, objectByteOffsets, bytes);
          objects.push(page);
          objects = objects.concat(getDependencies(page,objectByteOffsets, bytes));
          
        }
        
      } else {
        
        end = +end;
        for (var pageNumber = begin; pageNumber <= end; pageNumber++) {
          
          var pageAddress = pageAddresses[pageNumber - 1];
          var page = getObject(pageAddress, objectByteOffsets, bytes);
          objects.push(page);
          objects = objects.concat(getDependencies(page, objectByteOffsets, bytes));
          
        }
        
      }
      
    } else {
      
      range = +range;
      var pageAddress = pageAddresses[range - 1];
      var page = getObject(pageAddress, objectByteOffsets, bytes);
      objects.push(page);
      objects = objects.concat(getDependencies(page, objectByteOffsets, bytes));
      
    }
    
  }
  pageAddresses = [];
  for (var objectIndex = 0; objectIndex < objects.length; objectIndex++) {
    
    var newObjectAddress = [(newObjects.length + 3) + '', 0 + '', 'obj'];
    if (!Array.isArray(objects[objectIndex])) {
      
      objects[objectIndex] = [objects[objectIndex]];
      
    }
    objects[objectIndex].unshift(newObjectAddress);
    var objectAddress = objects[objectIndex][1].match(/\d+\s+\d+\s+obj/)[0].split(/\s+/);
    objects[objectIndex].splice(1, 0, objectAddress);
    if (/\/Type\s*\/Page[^s]/.test(objects[objectIndex][2])) {
      
      objects[objectIndex][2] = objects[objectIndex][2].replace(/\/Parent\s*\d+\s+\d+\s+R/.exec(objects[objectIndex][2])[0], '/Parent 2 0 R');
      pageAddresses.push(newObjectAddress.join(' ').replace('obj', 'R'));
      
    }
    var addressRegExp = new RegExp(objectAddress[0] + '\\s+' + objectAddress[1] + '\\s+' + 'obj');
    objects[objectIndex][2] = objects[objectIndex][2].replace(addressRegExp.exec(objects[objectIndex][2])[0], newObjectAddress.join(' '));
    newObjects.push(objects[objectIndex]);
    
  }
  for (var referencingObjectIndex = 0; referencingObjectIndex < newObjects.length; referencingObjectIndex++) {
    
    var references = newObjects[referencingObjectIndex][2].match(/\d+\s+\d+\s+R/g);
    if (references != null) {
      
      var string = newObjects[referencingObjectIndex][2];
      var referenceIndices = [];
      var currentIndex = 0;
      for (var referenceIndex = 0; referenceIndex < references.length; referenceIndex++) {
        
        referenceIndices.push([]);
        referenceIndices[referenceIndex].push(string.slice(currentIndex).indexOf(references[referenceIndex]) + currentIndex);
        referenceIndices[referenceIndex].push(references[referenceIndex].length);
        currentIndex += string.slice(currentIndex).indexOf(references[referenceIndex]);
        
      }
      for (var referenceIndex = 0; referenceIndex < references.length; referenceIndex++) {
        
        var objectAddress = references[referenceIndex].replace('R', 'obj').split(/\s+/);
        for (var objectIndex = 0; objectIndex < newObjects.length; objectIndex++) {
          
          if (arrayEquals(objectAddress, newObjects[objectIndex][1])) {
            
            var length = string.length;
            newObjects[referencingObjectIndex][2] = string.slice(0, referenceIndices[referenceIndex][0]) + newObjects[objectIndex][0].join(' ').replace('obj', 'R') +
                 string.slice(referenceIndices[referenceIndex][0] + referenceIndices[referenceIndex][1]);
            string = newObjects[referencingObjectIndex][2];
            var newLength = string.length;
            if (!(length == newLength)) {
              
              for (var subsequentReferenceIndex = referenceIndex + 1; subsequentReferenceIndex < references.length; subsequentReferenceIndex++) {
                
                referenceIndices[subsequentReferenceIndex][0] += (newLength - length);
                
              }
              
            }
            break;
            
          }
          
        }
        
      }
      
    }
    
  }
  for (var objectIndex = 0; objectIndex < newObjects.length; objectIndex++) {
    
    if (Array.isArray(newObjects[objectIndex])) {
      
      if (newObjects[objectIndex][3] != undefined) {
        
        newObjects[objectIndex] = newObjects[objectIndex].slice(2);
        
      } else {
        
        newObjects[objectIndex] = newObjects[objectIndex][2];
        
      }
      
    }
    
  }
  newObjects.splice(1, 0, '2 0 obj\r\n<</Type/Pages/Count ' + pageAddresses.length + ' /Kids [' + pageAddresses.join(' ') + ' ]>>\r\nendobj');
  newObjects.splice(2, 0, '3 0 obj\r\n<</Title (' + name + ') /Producer (PdfManipulation.splitPdf\\(\\), a Google Apps Script project by Jarom Luker \\(pricebook@hbboys.com\\)) /CreationDate (D' +
       Utilities.formatDate(new Date(), CalendarApp.getDefaultCalendar().getTimeZone(), 'yyyyMMddHHmmssZ').slice(0, -2) + "'00) /ModDate (D" + Utilities.formatDate(new Date(),
       CalendarApp.getDefaultCalendar().getTimeZone(), 'yyyyMMddHHmmssZ').slice(0, -2) + "'00)>>\r\nendobj");
  var byteOffsets = [0];
  var bytes = [];
  var header = '%PDF-1.3\r\n';
  for (var headerIndex = 0; headerIndex < header.length; headerIndex++) {
    
    bytes.push(header.charCodeAt(headerIndex));
    
  }
  bytes.push('%'.charCodeAt(0));
  for (var characterCode = -127; characterCode < -123; characterCode++) {
    
    bytes.push(characterCode);
    
  }
  bytes.push('\r'.charCodeAt(0));
  bytes.push('\n'.charCodeAt(0));
  while (newObjects.length > 0) {
    
    byteOffsets.push(bytes.length);
    var object = newObjects.shift();
    if (Array.isArray(object)) {
      
      var streamKeyword = /stream\s*\n/.exec(object[0])[0];
      if (streamKeyword.indexOf('\n\n') > streamKeyword.length - 3) {
        
        streamKeyword = streamKeyword.slice(0, -1);
        
      } else if (streamKeyword.indexOf('\r\n\r\n') > streamKeyword.length - 5) {
        
        streamKeyword = streamKeyword.slice(0, -2);
        
      }
      var streamIndex = object[0].indexOf(streamKeyword) + streamKeyword.length;
      for (var objectIndex = 0; objectIndex < streamIndex; objectIndex++) {
        
        bytes.push(object[0].charCodeAt(objectIndex))
        
      }
      bytes = bytes.concat(object[1]);
      for (var objectIndex = streamIndex; objectIndex < object[0].length; objectIndex++) {
        
        bytes.push(object[0].charCodeAt(objectIndex));
        
      }
      
    } else {
      
      for (var objectIndex = 0; objectIndex < object.length; objectIndex++) {
        
        bytes.push(object.charCodeAt(objectIndex));
        
      }
      
    }
    bytes.push('\r'.charCodeAt(0));
    bytes.push('\n'.charCodeAt(0));
    
  }
  var xrefByteOffset = bytes.length;
  var xrefHeader = 'xref\r\n';
  for (var xrefHeaderIndex = 0; xrefHeaderIndex < xrefHeader.length; xrefHeaderIndex++) {
    
    bytes.push(xrefHeader.charCodeAt(xrefHeaderIndex));
    
  }
  var xrefSectionHeader = '0 ' + byteOffsets.length + '\r\n';
  for (var xrefSectionHeaderIndex = 0; xrefSectionHeaderIndex < xrefSectionHeader.length; xrefSectionHeaderIndex++) {
    
    bytes.push(xrefSectionHeader.charCodeAt(xrefSectionHeaderIndex));
    
  }
  for (var byteOffsetIndex = 0; byteOffsetIndex < byteOffsets.length; byteOffsetIndex++) {
    
    for (var byteOffsetStringIndex = 0; byteOffsetStringIndex < 10; byteOffsetStringIndex++) {
      
      bytes.push(Utilities.formatString('%010d', byteOffsets[byteOffsetIndex]).charCodeAt(byteOffsetStringIndex));
      
    }
    bytes.push(' '.charCodeAt(0));
    if (byteOffsetIndex == 0) {
      
      for (var generationStringIndex = 0; generationStringIndex < 5; generationStringIndex++) {
        
        bytes.push('65535'.charCodeAt(generationStringIndex));
        
      }
      for (var keywordIndex = 0; keywordIndex < 2; keywordIndex++) {
        
        bytes.push(' f'.charCodeAt(keywordIndex));
        
      }
      
    } else {
      
      for (var generationStringIndex = 0; generationStringIndex < 5; generationStringIndex++) {
        
        bytes.push('0'.charCodeAt(0));
        
      }
      for (var keywordIndex = 0; keywordIndex < 2; keywordIndex++) {
        
        bytes.push(' n'.charCodeAt(keywordIndex));
        
      }
    
    }
    bytes.push('\r'.charCodeAt(0));
    bytes.push('\n'.charCodeAt(0));
    
  }
  for (var trailerHeaderIndex = 0; trailerHeaderIndex < 9; trailerHeaderIndex++) {
    
    bytes.push('trailer\r\n'.charCodeAt(trailerHeaderIndex));
    
  }
  var idBytes = Utilities.computeDigest(Utilities.DigestAlgorithm.MD5, (new Date).toString());
  var id = '';
  for (var idByteIndex = 0; idByteIndex < idBytes.length; idByteIndex++) {
    
    id = id + ('0' + (idBytes[idByteIndex] & 0xFF).toString(16)).slice(-2);
    
  }
  var trailer = '<</Size ' + (byteOffsets.length) + ' /Root 1 0 R /Info 2 0 R /ID [<' + id + '> <' + id + '>]>>\r\nstartxref\r\n' + xrefByteOffset + '\r\n%%EOF';
  for (var trailerIndex = 0; trailerIndex < trailer.length; trailerIndex++) {
    
    bytes.push(trailer.charCodeAt(trailerIndex));
    
  }
  var directory = pdf.getParents().next();
  return directory.createFile(Utilities.newBlob(bytes, 'application/pdf', name));
  function getObject(objectAddress, objectByteOffsets, bytes) {
    
    objectAddress = objectAddress.split(/\s+/);
    for (var addressIndex = 0; addressIndex < 2; addressIndex++) {
      
      objectAddress[addressIndex] = +objectAddress[addressIndex];
      
    }
    var object = [];
    var byteIndex = 0;
    for (var key in objectByteOffsets) {
      offset = objectByteOffsets[key]
      
      if (arrayEquals(objectAddress, offset[0])) {
        
        byteIndex = offset[1];
        break;
        
      }
      
    }
    object.push('');
    while (object[0].indexOf('endobj') <= -1) {
      
      if (/stream\s*\n/.test(object[0])) {
        
        var streamLength;
        var lengthFinder = object[0].slice(object[0].indexOf(/\/Length/.exec(object[0])[0]));
        if (/\/Length\s*\d+\s+\d+\s+R/.test(lengthFinder)) {
          
          var lengthObjectAddress = /\d+\s+\d+\s+R/.exec(/\/Length\s*\d+\s+\d+\s+R/.exec(lengthFinder)[0])[0].split(/\s+/);
          lengthObjectAddress[2] = 'obj';
          for (var addressIndex = 0; addressIndex < 2; addressIndex++) {
            
            lengthObjectAddress[addressIndex] = +lengthObjectAddress[addressIndex];
            
          }
          var lengthObject = ''
          var lengthByteIndex = 0;
    for (var key in objectByteOffsets) {
      offset = objectByteOffsets[key]
            
            if (arrayEquals(lengthObjectAddress, offset[0])) {
              
              lengthByteIndex = offset[1];
              break;
              
            }
            
          }
          while (lengthObject.indexOf('endobj') <= -1) {
            
            lengthObject = lengthObject + String.fromCharCode(bytes[lengthByteIndex]);
            lengthByteIndex++;
            
          }
          streamLength = +(lengthObject.match(/obj\s*\n\s*\d+\s*\n\s*endobj/)[0].match(/\d+/)[0]);
          
        } else {
          
          streamLength = +(/\d+/.exec(lengthFinder)[0]);
          
        }
        var streamBytes = bytes.slice(byteIndex, byteIndex + streamLength);
        object.push(streamBytes);
        byteIndex += streamLength;
        while (object[0].indexOf('endobj') <= -1) {
          
          object[0] = object[0] + String.fromCharCode(bytes[byteIndex]);
          byteIndex++;
          
        }
        return object;
        
      }
      object[0] = object[0] + String.fromCharCode(bytes[byteIndex]);
      byteIndex++;
      
    }
    return object[0];
    
  }
  function arrayEquals(array1, array2) {
    
    if (array1 == array2) {
      
      return true;
      
    }
    if (array1 == null && array2 == null) {
      
      return true;
      
    } else if (array1 == null || array2 == null) {
      
      return false;
      
    }
    if (array1.length != array2.length) {
      
      return false;
      
    }
    for (var index = 0; index < array1.length; index++) {
      
      if (Array.isArray(array1[index])) {
        
        if (!arrayEquals(array1[index], array2[index])) {
          
          return false;
          
        }
        continue;
        
      }
      if (array1[index] != array2[index]) {
        
        return false;
        
      }
      
    }
    return true;
    
  }
  function getDependencies(objectString, objectByteOffsets, bytes) {
    
    var dependencies = [];
    var references = objectString.match(/\d+\s+\d+\s+R/g);
    if (references != null) {
      
      while (references.length > 0) {
        
        if (/\/Parent/.test(objectString.slice(objectString.indexOf(references[0]) - 8, objectString.indexOf(references[0])))) {
          
          references.shift();
          continue;
          
        }
        var dependency = getObject(references.shift().replace('R', 'obj'), objectByteOffsets, bytes);
        var dependencyExists = false;
        for (var key in dependencies) {
          entry = dependencies[key]
          
          dependencyExists = (arrayEquals(dependency, entry)) ? true : dependencyExists;
          
        }
        if (!dependencyExists) {
          
          dependencies.push(dependency);
          
        }
        if (Array.isArray(dependency)) {
          
          dependencies = dependencies.concat(getDependencies(dependency[0], objectByteOffsets, bytes));
          
        } else {
          
          dependencies = dependencies.concat(getDependencies(dependency, objectByteOffsets, bytes));
          
        }
        
      }
      
    }
    return dependencies;
    
  }
  
}

上記コード(長いので折りたたんでいます)をこのコードで呼び出します。

code.gs

function merge(){
  const FOLDER_ID = 'hogehogehogehoge';//フォルダ ID
  
  //フォルダオブジェクト
  var folder = DriveApp.getFolderById(FOLDER_ID);
  //ファイルイテレータリスト
  var iteratorList = folder.getFiles();
  
  //マージするファイルオブジェクトのリスト
  var pdfList = [];
  //拡張子チェック
  var pattern = /.*\.pdf$/;
  
  while (iteratorList.hasNext()){
    var file = iteratorList.next();
    if (pattern.test(file.getName())){
      pdfList.push(file);
    }
  }
  mergedFile = mergePdfs(folder, "合体したPDFファイル.pdf", pdfList);

これで出来上がり。

#最後に
マージするPDFが多過ぎたりサイズが大き過ぎたりしたらタイムアウトしちゃうので、そういうのやる時は時間測りながらトリガー設定するなりしてうまくやらねばです。

ポッキーコーダさん(?がベースは書いてくれたっぽい)、ありがとうございまーす！！

#追記

パスワードかかってたらエラーになるのに加えて、Web表示用に最適化されててもエラーになることが判明。
PDFのバージョンも関係あるっぽい。1.4 (Acrobat 5.x)より前だったら良さげ。