there is no easy "indelible" on the ESP8266.
Either a value is fixed - than you can't change it or
it can be changed - than it can be deleted also.
If you are using the EEPROM emulation on the ESP8266, you just persist data to survive the next power down and you can retrive data on next runtime.
If you don't believe - show a short demo program demonstrating your problem.
If you do the sketch upload right, EEPROM data will survive.
if you decide to flash all, either provide also EEPROM data with your upload or don't be surprised that EEPROM is erased too.