I am an independant repair shop owner and have the capability to flash program as per J2534 protocol.
Have flashed a few Chrysler products.
If you take the car to the dealer, and have them flash the PCM, if you have an aftermarket tune, Your tune will be lost.
They can reprogram other modules on the car, and that won't affect the PCM, but I would not trust the dealer to not 'mis-communicate' between the service writer and the tech or whatever.
Reload the stock tune so you don't lose the performance tune when you go to the dealer.
Sometimes they will 'take the initiative' and flash the PCM just to be nice and update it for you to the latest calibrations (more for emission concerns than anything else)
Dodge dealer did that to me on some warranty work I had done on the Challenger. -didn't charge for it, which was nice, but did it without asking or anything.
Be careful.