Your Arduino duemilanove has a FTDI chip that converts USB to serial. It sounds like your excess voltage leaked from the pin to the supply rails and killed this chip. This is responsible for communicating with the PC and doing data transfer. It is likely that your ATMEGA chip is damaged but still managing to function although it's long term life time might have been shortened.
You need to replace the FTDI chip but sadly these are surface mount and not easy to replace.