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Unfortunately, it's not just a matter of picking a different network protocol for the sync. There's a shared database that each client syncs its own database with, and when you switch from MobileMe to Bonjour sync, you are pointing at a different database, which hasn't been updated while you've been syncing with the other method. That's why you get the warning about incompatible databases, because they are! You don't sync directly with your other client(s), but with that central database, though it doesn't necessarily appear that way if you don't look closely enough.

Previous versions used the local/remote terminology, and there was enough confusion that the current terminology was adopted.