Short answer- unless ECU is swapped out, your tuner doesnt care what tune is currently in the truck. Whatever the tune, it downloads it, flashes ECU with aftermarket, and stores the tune that was on the truck, whatever factory version that may be, and keeps that in its memory for you to take it back to stock should you need to.
Longer answer:
Your SCT tuner is married to your truck's ecu, so if you take it back to stock, and the dealer changes or does an update to your stock tune, it will not affect your ability to reinstall your aftermarket tune. If the ECU is swapped out for a malfunction, that would affect your ability to reflash from your tuner as it would no longer recognize it as the truck it is married to. The process of your aftermarket tune is this for your case-
It copies whatever tune is currently on the truck into its own storage, and then it uploads the aftermarket tune. The factory tune it downloaded is now in storage on the tuner. Then, when you flash it back to stock, Ford flashes an update to your stock tune, and you reconnect your tuner when you get the truck back. The process is identical- Tuner checks the ECU ID is correct, downloads tune on the truck (It labels this as stock tune, although the original stock tune was altered by ford) and then uploads your aftermarket tune into your ECU.