Very few dealers will not hassle you on it if you leave it in or were they can see it had been. A problem with taking it in with a program in it is that if there is a free update for the computer and they do it, you lost your program and will have to send it back to Banks to get the programmer un-vinlocked. I am not sure with the chips. It could possibly mess them up as well. I have never had any warranty work done. I don't think you would get any hassle out of things like exhuast or intake. Maybe others will know that have had warranty work done and have mods.