Jonathan suggest here: Xcode Includes .xib files that have been deleted! that cleaning all targets and empty the caches will fix the problem with Xcode including deleted .xi
In addition to doing the following, you may experience this issue if your app's Storyboard's files are localized. First, do each of these:
DerivedData
folder in ~/Library/Developer/Xcode/DerivedDataWhat finally worked for me was re-generating the storyboard localization files and deleting the English localization (which was unneeded because the Base Locale is English). To reload your Storyboard strings, see this answer on StackOverflow.
I had noticed that the non-text parts of my Storyboard were being updated, but not the localized text. If you have a localization in your app, I would recommend checking to make sure your localizations are updated (even if they're .strings
files).