I'm assuming that the battery was charged and then you used it long enough to where it would be expected to be discharged or close to it? With the SB and a 18650 battery people generally get about a day. Some people get up to maybe 2 days? Most people use it all day, put their second battery in and put the first one on the charger overnight.
Li-Ion batteries can be destroyed by overcharging, discharging them too far, and discharging them too fast. Overcharging and discharging them too fast can result in rather dramatic failures. Discharging them too far (running them down too low) can result it them not taking a charge any more. If the batteries are "protected" then they have a circuit that disconnects them in any of those conditions. A 3.7v Li-Ion is fully charged at 4.2v and as you use it the voltage drops. Minimum voltage (ummm, errr, I forgot... let's say it's something like 3.5v or 3.6v) when the battery is depleted is 3.6v. When the battery gets down to 3.6v the circuit disconnects it. This would be completely independent of which mod it's used in.