結論

import pptx, re
from pptx.util import Cm, Pt, Inches

self.replace_text('置き換えられる文字列', '置き換える文字列')

def replace_text(self, before, after):
    for shp in self.slide.shapes:
        if shp.has_text_frame:
            if before in shp.text:
                new_text = re.sub(before, after, shp.text)
                    self.replace_paragraph_text_retaining_initial_formatting(shp.text_frame.paragraphs[0], new_text)

def replace_paragraph_text_retaining_initial_formatting(self, paragraph, new_text):
    p = paragraph._p
    for idx, run in enumerate(paragraph.runs):
        if idx > 0:
            p.remove(run._r)

    paragraph.runs[0].text = new_text

参考元のコードだとforループの処理がうまく行われていなかったため修正

参考