Adding groups or moving files between groups in an Xcode workspace can result in files being deleted.
This _may_ just be an ObjectiveC legacy issue I hven't been able to confirm.
This fix is from StackOverflow but may help someone here:
But note you may have to add the enclosing folder/direcory back into the project before running the script if you see path not found.
git status | grep deleted | awk '{print $2}' | xargs -t git checkout
This is a critical bug and needs fixing urgently