Dude, call corporate and tell them the truth. They can not legally deny you any warranty work without PROVING that what you modified, is the cause of what you want warrantied. And unless you authorized them to remap the ECU, they also can't do that.
Almost sounds like the tech or the SA just wanted to make some easy money by doing an easy job that didn't even need done, while snaking out of the "hard" work by blaming your mods. I'd be furious.