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Your database on your Mac is still intact, right?

Assuming it is, and that you've configured your Mac to sync with your Omni sync server account, what you should do is to use the command File->Replace Server Database... to upload the database from your Mac to the server. Then, tap the sync button on your iPad to cause it to do a sync. At that point, you'll get a popup warning you that the databases appear to be incompatible, and asking which one to keep. You'll want to keep the sync database. After doing that, both devices should be in sync and you shouldn't have to do this process again.