Some chargers will not charge a Li-ion battery that is discharged too low in order to avoid a charging current that would be too high. Charging or discharging at too great a rate can lead to overheating, which causes a thermal runaway reaction commonly referred to as 'venting with flame'. What you need to do is measure the voltage across the battery. If the voltage is below 3V, then the charger may be designed to not charge it.
You can bring the battery voltage slowly back to greater than 3V by connecting it to another Li-ion battery in parallel (+ to +, - to -) with a resistor to limit the current flow. If you select another battery that has a voltage within 0.5V of the over-discharged battery, then the current will be low enough without a resistor. Remember that the resistor needs to be capable of handling the current flowing or it too can overheat. If the battery voltage is less than 2.5V then it is sustaining damage the longer you wait to charge it. It shouldn't take long to bring it back to the point that the charger will begin a charge cycle.
In the future, try not to rely upon the over-discharge protection of the batteries. That is really intended as a last resort.