Reflashing the stock-mode map with the AccessPORT installed would have the same effect as running the stock map as far as engine operation is concerned. That is, all the tuning parameters would be the same as stock. However, our proprietary code/data would still be on the ECU.
If you are doing this to take the car to a dealership and you are worried about the dealership detecting the flash, you need to uninstall the AP.
Bill