Does an un-rooted Android device still leave traces of the root?

I have an HTC Evo (original) which has a defective kickstand and battery door after about one year of use. For most of the time I have had the phone rooted, and love the features. Of the terms and conditions of warranty repair with HTC, however, one is that no unauthorized software be present on the phone. Naturally, this requires me to remove the rooted OS and return it to stock. The question I have, which I can't find answered anywhere else is: Does an un-rooted Android device still leave traces of the root? I'm not sure of the ClockWorkMod loader, or other software is able to be removed, cleanly without detection. If it is, do you have a concise tutorial on how to do so? If not, what do you suggest? Thanks!