So basically it's a 50/50 shot if I replace the Super IO and I need to see if a flash or eeprom links to it somehow. I also noticed that there is a footprint for a debug connector on the opposite side of the board underneath the Super IO with the lettering Jdebug4402 which I am guessing is for an external programmer.
EDIT:
I have located an W25Q128JV SPI chip that links directly to the Super IO. I think I'll try to replace it.