Is it possible to move the yaml files (except configuration.yaml) from the /config folder to /config/configuration_files and change the location reference in configuration.yaml?
I’m wondering because this are default configuration files, and I’m worried that Home Assistant wil make new ones after a reboot or upgrade.
yes
You should not move the defaults. However you can add your own as shown in this example: Splitting up the configuration - Home Assistant
So these ones cant be moved?
group: !include groups.yaml
automation: !include automations.yaml
script: !include scripts.yaml
scene: !include scenes.yaml
Sure they can, if you follow the format in the link or never use the UI.
For those interested, as Tom mentioned:
You can move the default configurations, and Home Assistant will still read them. However, if you edit them through the GUI, a new .yaml file will be created in the original location.