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I'm sorry, no offense intended, but if you're asking me that question after reading my description of the process, I think the safest course of action is for you to cancel the sync on the iPad for now, and call Omni in the morning. They'll hold your hand and guide you through the process.

Good news is that if you're getting that message, it means everything is set for successful syncing once the two are reconciled. The reason it seems such a bumpy start is that you've done the equivalent of buying a new computer, installing a bunch of software on it, creating a directory full of files, and only now wanting to try out the Migration Assistant instead of waiting for it to do its work prior to playing with the new toy.