Totally not so!
It would be VERY VERY rare for a dealer to reflash an ECU.
I have taken both my Limited and the SRT in for warrenty work both having custom ECU programs and niether have ever been reflashed.
ALSO you do not need to reflash your own with any cable if you feel uncomfortable you can send it back in and have the custom tuner reflash it for you, free of charge.
Don't worry they (the dealer) will not ever notice or screw you up.
Mike