Well the dealer has an 'out' Any change to the intake and you are out of warranty.
Personally i would NOT take it in with such a problem and an aftermarket part there.
Air filter is one thing, a different cai may be causing problems. And diagnostic is YOUR $$$. Since it is not stock.
If it were mine, i would have taken the new CAI off and gone back to stock to see if it is the problem.
For the dealer to see is going to cost you $$$ and maybe big money if they say your intake messed up something and voided the warranty.
Once they make that claim, You are screwed.
Naturally some dealers are more laid back, but i would not take the chance.