It all will depend on your dealer, my truck has never seen a dealer and never will now that the warrenty is out. But again its all in weather your dealer will look the other way or not. THe best thing to do is if your taking it in for a engine issue just throw the cat back on it only takes about 20 mins if you use a catless front pipe!
It all seems to depend on the truck wether or not it will set the egr code when the cat is removed. the two trucks i have done have set codes so we simply installed a Kennedy Diesel code blocker (aka Finger stick) to stop the code from setting!