Completely discharging a battery and leaving it that way is probably the worst thing you can do to one. The batteries are likely no good anymore.
Some older converters would only put out 10 amps or so to charge batteries. If you have 2 group 27 batteries that are fully depleted that's about 200 amp/hours. If your charger only puts out 10 amps it would take over 20 hours of generator running to recharge them.
The only way to know what's happening is with a volt meter; do you have one? If so, check the voltage at the battery terminals with the generator off and then with it running. It should be higher with it running, hopefully around 13 or 14 volts.