Allow EEPROM to be written or not using a definiitive command
The current method of refreshing or not refreshing the EEPROM uses a toggle command. While this may be sufficient or desirable for many users, it can be confusing when you are actively trying to get the firmware tailored to your situation and making minor changes to the config file as well as repeated passes through the configurator. In these cases, an option within the configurator and the config.h file to clearly update or not update the EEPROM is preferable.
Along with the possible uncertainty that the EEPROM is refreshed, there is also the very real situation that many users do not know when it is necessary to refresh it.
Another option would be to document exactly how the toggle mode works, when it works and when it doesn't!