What you edit in Arduino isn't the EEPROM. In pronterface after connecting, send the M502, followed by M500 to update the EEPROM with the new values. Marlin doesn't automatically update the EEPROM data, but the data in the EEPROM is used when the firmware boots up.
One of the items saved in the EEPROM is the steps per millimeter for the x, y, z and extruder.
One of the items saved in the EEPROM is the steps per millimeter for the x, y, z and extruder.