Hi Christina,
My understanding of the entire "version control" process is
limited but since no one else has thrown in, I will try to pass
along what little I know. What I have learned is that version
control works great until it doesn't.
What I've had to do in the past, when I've had these sort of
synchronization problems, is to remove the entire project from
version control (I would be sure to back up your local project as
well as your version-controlled project). Then, you should be able
to add the repaired project back to your source control software
(we use MS VSS but I think it shouldn't matter).
I have tried, in the past, to add individual files to the
database from the RH interface (you could try "check in all files")
and I have gone into the database and manually added the necessary
files, but I have had mixed results. In the end, it seems that
removing the project from version control, then adding it back, is
the only thing that is guaranteed to work.
Good luck!