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
I found another way in addition to command+option+shift+K. In XCode 4.2 there is an organizer that can be opened from top-right icon. You can clean all archives and saved project options from there. This helped my situation (I was seeing old removed files in the mainBundle).