It sounds like you're trying to merge two OmniFocus databases that were set up independently - the application won't do that on it's own. It assumes you want to use one database or the other on both devices, and keep them in sync from then on.
That said, it's possible to do what you're trying to do by hand. Go ahead and get the database from your iPad onto your Mac, then do the following.
- Select "Home" from the Finder's "Go" menu.
- Open the "Documents" folder, then the "OmniFocus Backups" folder.
- The backups in this folder are all time-stamped; double-click the one from just before you got the iPad's database onto your Mac.
- A new OmniFocus window should appear, showing the data that was on your Mac right before the iPad's database was synced over.
- You should now see two OmniFocus windows - one showing your "Real" database, and another showing the contents of the backup. Put both windows into the "All Items" perspective.
- You can now drag items you want to retrieve from the backup into the database that your iPad synced over.
Once you've retrieved everything from the backup, you can close both OmniFocus windows that are open. Next, restart OmniFocus; only your actual database will open up a window automatically. You can now sync the merged data back to your iPad and you should be set from here on out.
If you're still having trouble, though, our Support Ninjas are happy to lend a hand - if you send them an email
at your convenience, we can help.