"Conditioning" by full discharge should be done on individual cells, not on an assembled battery. Trying to "condition" an assembled battery will most certainly result in cell reversal, leading to irreparable damage to some of the cells.

The reason the charger refused to recognize the battery is because it must have been one of those "smart" chargers, which attempt to analyze the battery before charging it. In situations like that a simple "dumb" wall-plug charger is often the best approach to perform a slow "reviving" charge of the dead battery.