They will just overrite the tune. It happened for my Jetta that had stage 1 APR and I was REQUIRED by the state of California to get an ECM flash recall since it was related to "emissions". So I had to go to the dealer, have them flash my car with the recall update (which deleted the tune), get the paper saying its done then had to pay for the tune to be reinstalled.
I know that I shouldn't say add this to the list of reasons to get a Cobb AP. Pay once.