Well I cant say about my H3, haven't had any mods done on it, but I can speak for my Chevy Blazer's dealer workshop (still is a GM dealer)
First you're right they tend to blame anything and everything on a simple cellphone plastic holder on your dashboard
. they once blamed the AC compressor failure on my K&N kit regardless if the K&N documentation says it doesn't void your warranty. which is ridiculous, one has nothing to do with the other.
Anyway, I too changed the programming on the PCM only, with a Hypertech Powerprogrammer III, and everytime I take it for service, I simply make sure it's noted on the service card that the chip is re-programmed.
If anything they are working on (fixing) is controlled by a module (PCM or BCM) they will ask you to come in and change it back because their equipment will not function on a re-programmed chip. it will give them an error message sometime on THEIR equipment.
Conclusion : if it's regular service, you dont have to change it back. if they are fixing something and need to access one of the Modules, you'll HAVE to change it back.
Whatever you do, don't make the mistake my friend did on his 2001 Jeep wrangler, he tried to "hide" the fact he re-programmed his chip, dealer tried to access it, got an error message, went ahead and changed the entire PCM module and CHARGED him for it (part & Labor) heheheheh. Always make sure you mentioned the programming issue on the vehicle service card while delivering your vehicle for service.
SledgeHummer