Unfortunately, the error message you're getting means that two or more copies of the OmniFocus database have been superimposed on each other. We've had a couple of cases where backup software has done this rather than keep the various revisions of the main database separate.
Your first option would be to use one of OmniFocus' own database backups - by default, they're stored in your Documents folder.
If those aren't available, or if you find they have the same problem as your main database, contact the
support ninjas and they can assist.