You can pretty much take them down to 2.8V or even somewhat lower without worrying too much about it. Not that I recommend that. 3.1V is above almost all low voltage protection thresholds in lights anyway.
The cell should be fine. You may have lost a few potential charge cycles at worst. Glad to hear Dad is getting protected cells! You may have to explain how to reset them if all-nighters are his usual fare.
its fine. 3.1 volts won’t damage it. I have had many cells dip to the 2.7 volts range accidentally and charged up no prob. i have a few Panasonics that i recovered from a laptop pack that measured average between 1.9 to 2.4 volts, all of them charged up with no problems, never even got warm during charging, and all tested at near their rated capacity. ( been using them for over a year now in lanterns & flashlights.