Lipos can olny be discharged to a certain voltage per cell before it damages it. Normally I think you only want to use about 70% of the battery. you should charge it as much as poosible but every once in a while use it to 70% Just to give it a good cycle.

But Lipos do not get memory like NiCds or NiMh.

So I think what he is saying is that you may have drained it all the way down untill the battery was completely dead. Maybe the charger does not think its safe to try and recharge it, or the cell is damaged and the charger doesnt think its safe a damaged cell.