When a battery pack goes completely dead many times the individual cells have positive or negative charge that balances out to zero. This means some of the cells have changed polarity. In order to 'repolarize' the cells in the proper direction you need to pulse them with a pretty strong current in the right direction.
To do this just pull the pack out and hook it directly up to a 12 volt battery for about 2-3 seconds. Repeat this until the battery pack reads around 1 volt per cell. Do it too many times or hold the connection longer than 3 seconds and you will most likely destroy the battery pack. Then reinstall and charge normally. This also seems to remove 'memory'.
It is good practice to cycle the battery pack afterward to check if it is flyable.