I had a game earlier this year with a that had not scored a point ALL YEAR (we were in week 4, I think). I put the link to the actual TAPPS document in my phone just in case there was an issue. We started the clock to begin the second half (42-0 at that point). We had a foul early and there was confusion on whether they wanted to accept or decline the penalty. It took close to a minute to clear that up and the coach wanted time put back on. I said, "Coach, we do not put time back on a running clock -- it defeats the purpose!"He cried about the damn clock the entire second half, even though he complained before the game that his 4 best guys were out due to injuries and he was down to 13! Its really amazing how stupid some of these people can be.
Anyway, here's the actual rule from the TAPPS site:
MERCY RULE
1. In the event the score differential of an 11 MAN FOOTBALL contest reaches 40 or more
points, the following provisions are to be implemented.
2. First half time keeping will not be affected.
3. After half time, once the 40 point differential is reached, the Clock will run continuously
except for the following stoppages:
a. Time Outs
b. Quarter End
c. Injury Time Outs
4. Once the Continuous Clock has begun, time keeping does not revert back to normal
procedures even if the point differential is reduced to below 40 points
I wouldn't stop it after scores since it isn't expressly provided for, though the rule probably should include a "may" provision for Referee's time outs.