http://qiita.com/sassymanyuichi/items/ed32c5a10bdc1b799c6a と http://qiita.com/YoheiMiyamoto/items/57c7df1633bc62263835 を参考にプロジェクトを再設定してみたところ以下のエラーメールが来るようになった。

Dear developer,

We have discovered one or more issues with your recent delivery for "標高ワカール - 山登り・防災のための海抜測定". To process your delivery, the following issues must be corrected:

Invalid Swift Support - The Watch OS application has Swift libraries at both /Payload/Elevation.app/Elevation WatchKit.app/Elevation WatchKit Extension.appex/Frameworks/ and /Payload/Elevation.app/Elevation WatchKit.app/Frameworks/. Remove all of the Swift libraries from one of the locations and resubmit your app.

Though you are not required to fix the following issues, we wanted to make you aware of them:

WatchKit 1.0 - Your previous version used an extension for Apple Watch but your current version doesn’t. Users who haven’t updated their Apple Watch to watchOS 2 or later may lose access to their Apple Watch extension.

Once the required corrections have been made, you can then redeliver the corrected binary.

Regards,

The App Store team

https://forums.developer.apple.com/thread/17931 を参考にEmbedded Content Contains Swift CodeをElevation WatchKitはNOでElevation WatchKit ExtensionはYESにしてみたところ次のようになった。

Dear developer,

We have discovered one or more issues with your recent delivery for "標高ワカール - 山登り・防災のための海抜測定". To process your delivery, the following issues must be corrected:

Invalid Swift Support - The SwiftSupport folder is missing. Rebuild your app using the current public (GM) version of Xcode and resubmit it.

Though you are not required to fix the following issues, we wanted to make you aware of them:

WatchKit 1.0 - Your previous version used an extension for Apple Watch but your current version doesn’t. Users who haven’t updated their Apple Watch to watchOS 2 or later may lose access to their Apple Watch extension.

Once the required corrections have been made, you can then redeliver the corrected binary.

Regards,

The App Store team

これはおそらく、fasllaneでUSE_LEGACY_BUILD_APIを使っているため。そのため http://qiita.com/yoneapp/items/bc8e1fc6cafe79418f59 のように変更したところ次のようになった。

Dear developer,

We have discovered one or more issues with your recent delivery for "標高ワカール - 山登り・防災のための海抜測定". Your delivery was successful, but you may wish to correct the following issues in your next delivery:

WatchKit 1.0 - Your previous version used an extension for Apple Watch but your current version doesn’t. Users who haven’t updated their Apple Watch to watchOS 2 or later may lose access to their Apple Watch extension.

After you’ve corrected the issues, you can use Xcode or Application Loader to upload a new binary to iTunes Connect.

Regards,

The App Store team

これはWatchKit 1.0を切ったためにでる警告なので、無視しても良さそうと判断した。