That's to be expected? any modification you make, if it causes a problem, they aren't going to warranty the damage. For example, if your aftermarket air filter has a failure and comes apart, and some of those pieces get pulled in to the compressor of the turbo then they aren't going to cover the damage to the turbo (or anything else)
The other problem you have now is that even if you return the vehicle to stock it's still going to have that note against it. As a rule, if you want to keep warranty you'll want to swap out the aftermarket air box etc before taking it in for a service.
Also if they do see that Racechip they won't warranty ANYTHING in the drivetrain ever, even if you remove it
