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I checked in with the engineers. There's a bug that keeps the deleted files from getting removed from the database. Fortunately, you can force OmniFocus to clean up after itself.

1. In OmniFocus, choose Export from the File menu.
2. Choose a save location other than your usual backup location, so you can find this file again easily in a minute.
3. For file format, choose "OmniFocus Backup Document"
4. Save
5. Choose "Revert to Database Backup" from the File menu
6. Browse to the file you just saved in step 4 and click Open

Once your main file is down to size and you're ready to start syncing again, I recommend moving aside the OmniFocus file that is currently on your server and resetting the database on your iPhone so that OmniFocus can have a fresh start.