I also have the same charger and have recovered a couple of batteries from over discharge only, and I would just throw out any battery that was damaged. First I put everything out on the drivway, never in any building, NEVER! Then I charge through the output lead on the battery on the Nicad setting at 1 amp and set the timer for 10 min, I attach my cell tester to the balance tap to monitor the voltage and stay with it while it's charging. When the timer goes off I let it sit until the voltages stabilize, and then start it over again. Once they all reach min voltage again I go to the normal balance setup and finish charging. Whats been said before is correct, the battery will not hold it's charge as well as before but since I use it in a transmitter it's not in a high drain situation and I just have to remember that my low voltage alarm will not go off until it hits 8v which is too low for a 3 cell lipo. LiFe batteries can be brought back in a similar fashion but if your not comfortable then discharge them and throw them out. They cost too much for me to toss them though,just because I made a mistake once and let them get too low. Very good battery info here
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