Do you mean save the eeprom data memory but rewrite the flash program memory?
Can't you just read the eeprom data, save it to a file, and them load it back in with the new flash code? This should work unless the chip is code protected; then you are in the realm of hacking and I can't help you there.
Do what I did... Get a PicKit2 programmer.. I can program the EEprom and normal flash areas completely independently of each other using the stock software.
IcProg is a great free utility, but does have limitations.