The usual problem when this happens is the charging current initially is more than the charger can handle, so it crowbars thinks it has been shorted out. The fix is to insert a resistor between the charger and battery pack such that the the current through the dead battery will be equal to less than the normal charing current, and let it charge that way for a while.
So for example a 16 cell pack would normally charge to about 24 volts, If you put a 500 ohm resistor in series, that will limit the charging current to about 50ma initially, (and is unlikely to seriously overheat the resistor). Within a few minutes, the batteries will no longer be completely discharged, and you can take the resistor out of the circuit.