When you make changes in the UI and save them, they are saved in /data/configuration/system_hardware/rotaryencoder2/config.json.
Please note, that there is another version of the file under /data/plugins/system_hardware/rotaryencoder2/config.json, which is not changing when you save, because it is the ‘reference’ version of the file, which stays always “as installed” - U can e.g. use it to go back to the default, when something is messed up.
If the file in the configuration folder is really not saved, then please report back, because then I will need to upgrade my test-system to the latest Volumio version and see what changed.