Say the user somehow managed to delete my application’s core data store. (Which has been previously synced with sync services to Mobile Me.)
How do I tell core data to pull the truth (or to refresh) instead of fast sync?
Core Data + Sync Services: How to refresh / pull the truth?
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If they deleted the persistent store, they probably deleted the fast sync store as well. Even if they didn't the application should do a slow sync and pull everything from the truth on next launch.
You should not need to do anything special, from the Sync's PoV it is a new client coming online to sync.
Naturally I would test this in a dev environment first to confirm but it should not require any changes.