If they reflashed your vehicle then u may have a problem there. The proper procedure should have been to return to stock before going to the dealer then if it was reflashed you would have to upload that new stock tune and send it to mpt. Then they would send you new tunes for your updated stock file.
I reflash to stock prior to taking the vehicle in, but wasn't notified of a dealer flash/reflash. Highly doubtful I would have been notified....