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One additional detail: if you're on the Mac that bonjour syncing is using as a server, there are actually two copies of your OmniFocus database. The one Andrew pointed out is one.

The other one is stored in a "Synchronization Data" folder in the OmniFocus folder he referred to. Your phone talks to the Synchronization Data copy, and then it gets moved over to your 'real' database in the location Andrew mentioned.