after you tune your car, if you take the tuner back inside and plug it into the computer and open up the SCT program, on the main page it has an option to download your stock file.
I did it from day one, because you never know when you might need it.
example, I had the car completely brick once, wouldn't start, wouldn't accept a tune, wouldn't do anything but flash every light on the dash. I called SCT and they had me send them my stock file I backed up, along with reformat and reset my tuner, then loaded that file on my device and I flashed it to the car and recovered perfectly.
Had I not had that file, they said I "may" have had to take it to a Ford dealer to have the PCM manually reflashed.