I managed to fix this at last but will leave the thread in case anyone else needs it.
My fix was in the project folder in - intermediate/source there are 3 files with .build .cpp and .cs extensions. For some reason there were 3 version of the old filename and 3 versions of the new file name. Deleting the 3 with the old file name fixed the package error.
Not sure why they would be copied with old filename and not renamed during project clone but UE4 is funny like that ay.