I had the same problem - which appears to be the path of the file (in the .pbx was not correct because of case sensitivity.
If you look at the file's "File Inspector" (i.e., the window on the right of the code), see if the path shown matches the exact path (case sensitive) of the file's location. Mine had a lowercase letter for the folder (e.g., "/foo/..") but on the OS it was actually "/Foo/.."
I quit Xcode, then using a text editor I use searched my project.pbxproj for "path = foo". I found it in a section listing my problematic files. Change it to Foo.
Start Xcode, load the workspace, do a clean and everything seems to work