[BigNoid]

When it becomes available you should remove the SublimeKodi folder completely from your addons folder and just rename your custom settings file in User/ subfolder to kodidevtoolkit.sublime-settings.

Not sure if its because I installed manually, but I had to remove the kodidevtoolkit.sublime-settings (after I renamed it from sublimekodi.sublime-settings) and recreate it through the package settings for getting the settings to stick.