They changed TOT a few weeks ago to where it doesn't start counting until there has been an hour of inactivity. So basically it's gone unless you're a jerk off who likes to try and push the limits.

But to answer your question, I have seen this asked before an someone claiming to be an AM chimed in and said that it doesn't stop TOT but instead flags your name for something else, I forget what exactly, and they can't excuse the time you were gone if you were gone for a legit reason because your scanner was constantly scanning something. So like if you had diarrhea and were gone for 30 min then they can't excuse the time if you had the sp00's scanning.