Depends on your implementation. Normally, the undo manager open an undo group for your event and encapsulates the changes, see groupsByEvent. If you use a secondary managed object context for your background synchronization and merge the context back in to the main context you have to ensure that you disabled the undo registration, see disableUndoRegistration.
Edit: Here is a little code snippet with that you can synchronize in a separate context without creating undo actions
// create a child context with no undo manager
NSManagedObjectContext *context = [NSManagedObjectContext contextWithParent:self.managedObjectContext];
context.undoManager = nil;
[... do your synchronization with the child context...]
// merge into main context without generating undo actions
[undoManager disableUndoRegistration];
[context save:&error];
[managedObjectContext processPendingChanges];
[undoManager enableUndoRegistration];
// to prevent undo action beyond the synchronization to remove all undo actions
[undoManager removeAllActions];