How did that happen? It was used in a 3AAA application and it got left on. They were not at exactly the same state of charge so the least charged cell depleted first and went into polarity reversal meaning that the remaining two cells were now charging the dead cell backward.
NiCd's didn't like being reversed either. In fact no cells tolerate that perhaps except lead acid under very strict conditions.
Under discharging tends not to be a very big deal - that is discharging the cell very deeply. Even as low as near 0 f.ex. in a single cell incan light - as long as it's not reversed and not stored for days or weeks afterward.
However it can be a problem getting some modern -dV chargers to recognize cells and/or get them to charge them. Just give the cells an hour in a dumb slow and/or timer based charger and switch them to a -dV one.
I don't know what application you've used to destroy the cell. But let me give you and others in same situation an idea.
I have a similar application myself with 3 NiMH cells. It's regularly run until flat so not to destroy the cells I've got the idea to use a LiIon protection circuit. It is so luckily that it also happens to cut off when 3 NiMH cells are empty but before the weakest one is pushed in reverse - even if you put in a fully depleted with two freshly charged. Those cells are 2 years old and probably has got something like 200 cycles on them - they're still like new thanks to the protection circuit.
You can even use the idea with more cells. However it has to be in multiple of 3. as you implement a circuit for each 3 cells.
You can get loose protection circuits from DX or take them out of old LiIon like cell phone and camera batteries (single cells are easier to work with). Just take care not to short the old LiIon cells as we don't want anything nasty to happen. The cell phone ones are however not very high current capable but fine for many things. Before throwing out the LiIon cell I took the circuit from I discharged the cell completely to practically 0 V with a 10 ohm resistor so it won't go
in some battery container (remember it's safe to discharge LiIon to 0 V - it is however not safe to charge them again from that state).
