I've never been faced with a situation where the trailing team started to catch up and wanted to go back to regular time but if it should occur, the rule states : "...By mutual agreement of the opposing coaches and the referee, any remaining period may be shortened....". I would take that to mean we no longer have mutual agreement and regular timing would apply.
I would think you should have a rule to cover that. I interpret the "mutual agreement rule" the exact opposite way: we had mutual agreement to shorten the game. Whether we still have it or not is immaterial, we had it, and we did it.
I see arguments for both sides, which is why it should be covered in the rules AHEAD of time, and not left up to interpretation when you get into the situation.
While I don't completely agree with our rule, at least we have one: however you start the quarter is the way you end it, and once you start the running clock, there is no going back. So if a team is ahead 29-0 at the start of the 4th quarter, there will not be a (legally) running clock, even if the score gets to 50-0. It's only the status at the start of the 3rd or 4th quarter that matters. Conversely, if it's 30-0 at the start of the 4th quarter, you will have a running clock for the whole quarter, even if the losing team scores three TDs in the next 5 minutes.
I don't completely agree with it, but you can't argue about it, it's written in black and white.