[cmalin]

Replying to my own post. I seem to have fixed things, so I wanted to share the result in case someone else is still having a problem.

First, I turned off sync on the desktop. Next, I copied the iDisk sync DB to a safe place and then deleted the original from the iDisk. I had to sync the iDisk to ensure that the old DB was really gone. Then I reset the DB on my iPhone (so it deleted that DB) and then used "rebuild database" from the file menu of the desktop version of OmniFocus. Finally, I turned on syncing on the desktop again, and everything appears to have worked.

Oh, then I went back to the iPhone and performed a sync. I may have made some changes when I was first messing with this, so the iPhone asked me if I wanted to use the local or server DB. I chose server, since I knew that was the one I had just fixed.

That's it.