Just a thought... Would it be possible to have the bootloader copy data in eeprom into flash on reset? So it would go something like this...
reset
bootloader copies value of eeprom into an area of flash after existing program and deletes eeprom
during program, save something new into eeprom
repeat
Although I'm not sure how you could delete old info you don't want anymore that is now in flash. Does this seem doable? Has anybody already done something like this?