This sounds like the eeprom will contain all the flash logic and will switch to eeprom loop in case there is no data on main flash. Like mini boot loader.
ON flashing you can even use code from there and only upload flash content.

On sure how it will work on eside. Might need some reconfiguration and possibly one time patch. But it will be totally bulletproof, once you figure how to switch between main flash and eeporm boot logic.