Your best bet is gonna be take it to a shop that has a IDS. In the IDs you have to go to install a new module, it will check if there are any later pcm or tcm updates, if so it downloads them erases the current programming in the module and reprograms. It usually will reflash the pcm tcm and any other module it needs to update.
So if the truck has a tune on it would you need to return to the stock tune, reprogram the modules, the reload the tune?