Technically, yes. However, if you have a dealer that will work with you on that, then you can get away with it. You really can't do much of anything to these quads without it voiding the warranty altogether which is really stupid IMO. If the mod (in this case) causes another failure, then the warranty should not cover that failure. However, if the mod has nothing to do with a failed component(s), then it should be covered. Many dealers will agree....let's hope yours does.
It also depends on the warrenty work.If its something say your fan takes a dump or your brake rotors crack.If he or she is not in looking at your clutch I would say they dont need to know.Because the way most shops run they arent going to be looking somewhere that is not connected.Just my 02 cents.