The explanation here is EEPROM. If you ever used Chrysalis, that copied the then active layout to EEPROM, and flipped a setting so that the EEPROM layout will be used over the built-in one. So no matter what you change in firmware, as long as the EEPROM-Keymap plugin is enabled, and the setting isn’t reverted, it will use EEPROM over the built-in.
The easiest solution here is to launch Chrysalis, connect to the Model01, go to the “Keyboard Preferences” menu, disable “Use custom layers only”, and hit the save button. It will then use the built-in layers instead of the EEPROM-stored ones.