Bundled framework issues with Bitcode compilation

I have a watchOS app which includes a framework. Suddenly with Xcode 7.3, I have been having issues with Release builds.

I had to follow the manual instructions found here to solve my Release build issues. My app compiles on all build configurations now. When I try to export my app from the Xcode Organizer, I'm faced with other errors.

From the very verbose console output, I found the last error message in the process:

description = "failed to compile bitcode for Coventry-Watch:\n Debug: SDK path: /Applications/Xcode.app/Contents/Developer/Platforms/WatchOS.platform/Developer/SDKs/WatchOS2.2.sdk\n Debug: PATH: ['/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin', '/Applications/Xcode.app/Contents/Developer/usr/bin']\n Debug: Using: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/lipo\n MachoInfo: cd /\n \"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/lipo\" \"-info\" \"/var/folders/bk/lqjcpcfx0g1g2_k4bp49ppq00000gr/T/ipatool20160331-56415-1e0ofzg/thinned/armv7k/Payload/My App.app/Watch/My Watch App.app/PlugIns/My Watch App Extension.appex/Frameworks/Coventry-Watch.framework/Coventry-Watch\" \n ...

I can't work out what has changed in between Xcode versions to suddenly cause an issue. I think I understand the error, but I don't know what might need fixing to resolve it.

From the link you provide, I understand that the framework included by your app is "built by an Aggregate target, which has a custom Run Script to build a "fat" (simulator+device) version of it".

If this is the case, your bitcode-missing issue may come from the same problem described in this question. And the workaround for it is to add the following line at the beginning of your Aggregate target script:
unset TOOLCHAINS