It is not difficult to damage a protection circuit, by dropping the cell or by applying excessive spring pressure (>15 lbs). The circuit sits on the end of the cell, and being a small printed circuit board, it is actually quite fragile.
As long as it is treated carefully, it will be fine. Problems can arise when people rely on the protection circuit too much, and think it will always protect against every adverse eventuality. Damage to a protection circuit is not always obvious or visible.
10mm diameter cells (10440s, 10280s, 10180s etc) do not have protection circuits, as there is no circuit currently made that is small enough to fit them. Users of these cells have to understand the risks.
It can be more dangerous to discharge unprotected cells slowly, as the dimming of the light as the cell empties may be gradual, and not so quick and noticeable as it would be at a high discharge rate. Also, with a slow discharge rate, the voltage sag will have been less, so the cell will not always recover adequately.
It is worth repeating here that Li-Ion cells are fully-charged at 4.2V, and effectively empty at 3.5V (resting voltages). It is better to recharge a Li-Ion cell before it drops to 3.5V resting.
Maximum life for a Li-Ion cell will be achieved if it is operated between 3.6V – 4.1V.
Users should always keep careful track of run-time and remain aware of the state of charge of their cells.
Damage will have occurred to a Li-Ion cell if its resting voltage is below 3.0V, especially if it is left at that voltage for an extended time. Recovering an over-discharged cell is possible, but the correct procedure for doing this is not without risk, and not always successful. The incorrect procedure (putting an over-discharged cell on a charger for a normal ~0.5C charge) is very risky, and this is when most over-heating and venting incidents can occur.