It's possible that this will work just fine if you're extremely careful, but it's not a workflow that the design of the app takes into account. The error messages you're seeing are basically OmniFocus noticing that there are some files in the sync database that don't make sense to it.
The best thing to do is probably contact the
support ninjas. We're happy to help get the database straightened out, and then help you set up either WebDAV or disk-based sync with a minimum hassle-factor.
Hope this helps!