Curious about dealers, hex codes and tunes

[Longshot270]

I was reading through posts about how if you do not set your truck back to stock the dealership could really mess stuff up with a reflash. This part I understand. But it got me wondering, if they reflash the truck after it is set to stock, doesnt that change the current hex code? If it does then isnt there going to be trouble with the tunes? I dont really know because everyone I know with a programmer or code reader do their own work and never go to dealerships.