First off how can you add a cold air intake if the car already comes with one? If you are talking about something like a ram air intake or some modifications done to the stock intake system... I do not see how it can possibly void the warranty as this product only in the most extreme cases can do any damage to other components... maybe if you close of an intake and disable the car from breathing in any air... through them... is the only way I can see it doing damage to the engine...

Unless the dealer is able to prove that a modification is the cause of the error your warranty will not be voided... warranties do not get voided too often and are not voided that easily... unless you add a high boost supercharger and not balance the engine towards it's expectations it is not a really easy task to void the warranty... especially with the current aftermarket parts available for our cars... and the limited experience our chrysler mechanics have on our cars...