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
You have to be careful about the xib file. I tried all the above and nothing worked for me. I was using custom UIButtons defined in the xib, and realized it might be related to the fact that I had assigned attributes there which were not changing programmatically. If you've defined images or text there, remove them. When I did, my programmatic changes began to take effect.