OK, my first advice is that if you're worried about potential data loss, make a backup before you do something that might risk that data. That way if something happens, you can always restore from your backup. (In General Preferences, you can tell OmniFocus to back up twice a day, and to also back up when quitting.)
I'd love to figure out what went wrong so we can prevent it from happening in the future, but first let's just get you back into a good state. Connect to your iDisk, and move all of the OmniFocus-related stuff from the Document folder into an archive folder that we can examine later.
Moving that stuff out of your iDisk documents folder means that your synchronization should be back in a pristine, original state. Synchronize from your desktop to make sure that works. Maybe synchronize one more time to make sure it still works. If you look at your iDisk at this point, you should have a single OmniFocus.ofocus folder inside your Documents folder, you shouldn't have any "copy-in-progress" files lying around.
Now go to your laptop, and sync there. It may prompt for you to replace your local copy with the server copy; if so, say yes. Sync again, to make sure that's solid. Go back to your desktop and sync there.
Everything still working? Try changing something, and sync on both sides to see if the other side sees the change.
Now try adding your iPhone to the mix. Try changing something and see if it changes everywhere following a sync. If any of these steps fail, please let me know which one and how it failed.