Eeprom stays the same. The idea is if you need to change something stored in eeprom that you do NOT need to upload. Instead change it in eeprom with eeprom editor. In parallel you could change it in config so in case eeprom is lost you have same data. But it is just a pain to upload instead changing directly.
In addition with
M502
M500
you can copy config values to eeprom any time you want even if you do not change EEPROM_MODE. EEPROM_MODE change just enforces this on first start.
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