keyboard/qmk/quantum/tools/readme.md

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`eeprom_reset.hex` is to reset the eeprom on the Atmega32u4, like this:
dfu-programmer atmega32u4 erase
dfu-programmer atmega32u4 flash --eeprom eeprom_reset.hex
You'll need to reflash afterwards, because DFU requires the flash to be erased before messing with the eeprom.