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If you are in a situation where the files that are being shown have been deleted from the project navigator view but it still seems to be showing up as somehow linked to the project, even though the file no longer appears in the Project navigator, you must remove also from the svn in order to resolve the warnings.
Just open the Terminal utility, browse to your folder where your .h/.m files located and type the following command:
svn delete nameOfMissingFile
Update: Mountain Lion users check this!
Very helpful, thanks a lot!