I have an 04 Ram Hemi that was at the dealership last week. They had fixed the cruise control and now the programmer is locked out since I forgot to change it back to the factory settings. I tried downloading the latest programming, but it still won't allow me to change any settings on the vehicle.
Don't know about your Dodge, but in the Ford world if the dealership "re-flashes" your computer (to upgrade it, for example) you're out of luck, and will have to pay Superchips some amount of $$ to reset your programmer. This is how they (and other companies) prevent people from buying one tuner and then "sharing the wealth" with everybody they know.
Unfortunately, it sounds like you're learning an expensive lesson... By the way, you may have much bigger problem if the dealership discovered the "tune" before erasing it ... they may have voided your warranty -- sure hope not!!
You'll need to contact Superchips directly to get the programmer back up and running.
'05 Ford Excursion Powerstroke 6.0L, Flashpaq 1805
"The world is round ... we'll get there!"