You are right, entries of cfg files are only added/updated, but other/older entries are not deleted automatically (because they might have come from a different source, so it might be dangerous to delete them).
Instead of manually messing around the cache folder, you can simply use the console to clear your configuration. Do a
openhab> config:list
and you will see all configs that are set in the system. To delete one, simply do a
config:delete org.openhab.weather
Hope this helps!