You should mention something about storage. Please clarify if the batteries are ticking bombs which will explode when the discharge under 3V...
No that wont happen, worse case is when they are charged from a low voltage. Most cells these days have a minimum low of 2.5v(some 2.8v). Its not recommended to go bellow this voltage. If you do, charging asap is key and not to leave for long periods..............this over time causes a build up due to the chemistry inside and can go south when charged.
Store around 3.6v in a cool dry place if for long periods. If in a flashlight, lock out to eliminate any parasitic drain and check periodically . Even if it means running the light for 5m and topping back off or leaving around 4.1v which can help the life over time(years).
When a cell is shorted, this causes a risk and with the pressure inside(pipe bomb), so not only are voltage checks important over time, but also checking over the cell, making sure the wrap/s are not torn/damaged.................if so, remove and replace with readily available wrappers (cheap as chips). Many youtube vids to show how easy to fit..........I slip one on the cell, check length which usually is a few mm too long, remove and cut off with scissors. Re fit on the cell, heat with hair dryer(carefully) to shrink wrap on cell.............check all is well and good to go again.
Not into great detail, just keeping it simple like me

but those are some basics.
Too add, there are usually lots of warnings even if a flashlight will not flash or blink when close to 3v. Not being able to get into higher modes is a simple indication to charge back up. Ideally, try and not go bellow 3.3-3.5v to keep it within a nice margin of possible...........how will i know when its 3.5v???? Well if a new light, use for a set period, check voltage and repeat to get an idea. For example it may take 2hrs of use to get to 3.5v on medium and turbo uses. So if your uses is simply 30m a day, every 4 days top cell off(just a rough example).