I'm not sure but I think if they update your ecu it is based on the stock tune. If you have a custom tune in there, the update won't relate to it. Plus your stock tune stored in the programmer won't get the update. I have heard both sides of disconnecting the battery. I didn't last time I went in for an oil change but, it does sound like a good idea. I just try to play it safe and flash to stock whenever I go to the dealer.