If you're trying to charge it as a lipo, most chargers will not charge if the voltage is below 3v/cell or 6v for a 2S. This is a safety issue.

You can charge it as a NiMh at a low rate like 0.3-0.5amp just long enough to get the voltage back up over 6volts. Make sure you monitor this charging as if left alone it can potentially result in a fire. It is safe to do as long as the lipo doesn't swell and you stop it when you see thevoltage has gotten above 6volts.

Soon as it gets over 6v, stop the NiMh charge and charge it as a lipo. It should now charge. I'd charge at a low rate like 1amp to help the cell that was low 'catch' up. There may be some diff between cells when its charged. You'll just have to wait and see how much. This lipo may need a few low rate charges and discharges to get both cells to read the same.

I had the same issue with a Turnigy 3S - one cell was .42v and wouldn't charge. Its fine now after doing this same kind of thing with mine.