Your stock file is stored during the initial programming process. The stock file stays on the programmer until the vehicle is returned to the stock tune.
Returning the vehicle to stock will 'un-marry' the device and allow it to be used on other vehicles if desired.
To use custom tunes on another vehicle with the same device, a new tune file will need to be created and loaded onto the tuner. For BAMA Performance customers, this would mean re-enrolling in the Free Tunes for Life membership for the new vehicle.