If it's anything like my Subaru, the ECU has a core map which can only be flash when the engine isn't running and a real time map in which things can be changed on the fly or real time. So yes if it was tuned, the dealer should be able to flash your ECU with a current factory program.
Core flash = can not be erased just by unplugging the battery - has to be re flashed.
Real time = yes this can be reset to what the core flash or base map is set to just by unplugging the battery.
Base map has all the basic parameters, while the real time maps gets updated with driving habits and environmental variables. Open/Close loop - detonation/ping detection