Plugin checks your .yml files versions and if your files are olds the plugin will automatically update them.
This can be not user-friendly
New things will appear on bottom of their path.
The auto-update does not delete the older comments on the .yml files.
For a better update its recommended make a copy of your .yml already configurated and delete the olds, restar the server to create the new ones and then reconfig them with your copy.
This can be disabled on the new config.yml, files-auto-update: false | true
If you leave this on false make sure to update manually yours files on every plugin update or this could cause bugs.