Li-on should be stored at about 50% charge. That should last for months>years. Stored for me is anything over a week. If you are less conservative change that to a month. But they fare better if not stored fully charged. At LEAST get them down to 3.9-4.0v/cell for sitting around.
A light "system" with Li-on batteries REQUIRES some kind of cut-off (PCB), either in the light head driver, more likely in the battery. If, for some reason the pack gets down to cut-off level, it should kick in and stop the current. BUT, when current is applied in charging it should disengage and allow charging. You CAN get a failure of this PCB cut-off electronic. You can get a failure of the charger to deal with the low battery. I've seen 2 PCB fail. Personally I don't much like them because they generally don't balance the batteries. If the batteries are not well matched they get more out of balance with use until they fail. But, without a PCB circuit you really need to have a balance tap, a charger that can deal with it, and KNOW what you are doing. So, for most people the protected battery pack is the way to go. Mostly you don't have much of a choice.
Like a lot of electronics most of this stuff is made in China and you can get excellent, decent, mediocre, and damn poor electronics. I suspect your PCB failed, and the batteries are sitting in there just fine but you can't get at them.
NOTE - An NiMh battery needs entirely different care. Charge after use. Top regularly if not used routinely. Cycle occasionally if not used regularly. To my knowledge no one is using top grade LSD type cells in NiMh packs for lights. If they did, those would have even different care.