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I used to get that, especially if I messed up and allowed more than one instance to be "active" at the time of a sync… oh, and I do NOT "sync", I do a "backup," thus completely overwriting any files that do not match the current "live" state.

The way I resolved those issues was to clean out the "bad" OmniFocus.ofocus file and restore the DB from backup.

Hope that helps...

J