I had a file which I deleted and replaced with another file, somewhere else, of the same name.
Despite cleaning, and trying this multiple times, I keep getting this
Got the similar troubles.
It seems XCode does not generate correct relative filepath when your project refer to an already existing source tree (relative path does not contain the .xcodeproj in the path of the file to be compiled).
There is a simple fix however: in the project explorer select the file or files files then look at the options in the file inspector. One of them is labeled "Location"; set it to absolut path and try again. This fixed the issue for me :)