I'd try an see what was wrong personally, but I have experience fixing probs like that too.

If it doesn't matter, then harvest the connector if its worth re-using buy a new one.

Just so you know, lipo capable chargers will not charge a lipo that reads below ~3volts/cell (6v for a 2S) due to potential safety concerns. The low voltage is why the charger is doing what its is doing.