The thing to understand is if you rename a setting (resourceKey) it does not update the existing setting it is the same as creating a new setting. Once you rename it in the config file there is nothing there to tie it to the previously created setting. So if you rename a setting (or remove one) in your custom feature you should implement an upgrade script to delete the old one from mp_ModuleSettings and mp_ModuleDefinitionSettings making sure to use your featureGuid in the where clause so that no settings with the same name from other features get deleted.
Hope it helps,
Joe