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Syncing your iPad to iTunes should make a backup of all the data on the iPad. However, I've read lots of complaints about iTunes' restore feature not restoring user data.

If you're syncing OF to a server (see OF iPad gear menu, sync settings), then that serves as a backup. If not, then I'd recommend copying the ofocus file from the App tab in iTunes occasionally. That will give you a backup that iTunes won't mess with. (Still, it would probably be better to get an account on the Omni sync server and set up automatic syncing of OF to the cloud.)
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Cheers,

Curt