In my project, I\'ve include a full \"shared\" folder by link (not copy) that is outside my project folder.
In the .pch file, I have #import \"MyStandardHeader.h
I've seen this too: files that clearly exist get wonky. Oddly, sometimes it fixes itself. It may be an Xcode bug, since the build always succeeds. I've had success with touching the file. sometimes a clean helps. and sometimes quitting xcode helps.... Voodoo really.
You could try to remove the index by deleting everything in ~/Library/Developer/Xcode/DerivedData
That directory is a combined version of the old Build and Intermediates directories from Xcode 1,2 and 3. Basically it's all the temporary and generated files from your project: object files, indexes, etc.