After updating my POD install, Xcode sprouted a new issue:
I experienced the error when overwriting project.
Still encountered the error after:
Changing the clang settings
ionic cordova platform remove ios rather than just delete ios platform folder before each new build (and of course add the platform again)
updating ruby as per instructions: https://forum.ionicframework.com/t/x-code-8-beta-2-apple-mach-o-linker-id-error/71998
Error was solved after changing to a different branch in github but perhaps one of the other troubleshooting methods played a part. Now all branches run on xcode without the Mach -O Linker Error.