Anyone know if it works to simply erase the eeprom, or does it have to be loaded with specific information? If erasing it works, that's pretty easy, something like a Bus Pirate, or even just a microcontroller can easily talk to a serial EEPROM, they're quite standardized parts. If you don't want to bother with that, you can buy new blank parts for ~50 cents and simply replace it.

I wouldn't recommend even trying to restore any type of lithium battery that has been deeply discharged. They are notoriously fickle and easily damaged by discharging too far as well as overcharging. Having seen the results of several lithium batteries that caught fire, I would err on the side of caution and throw out the dead cells.