Try
the manual for help on the CLI tools.
As for the "losing your settings" thing, you either want to use your Kindle with Calibre, in which case disabling the plugin would be unwise because Calibre wouldn't recognize the device any more, or you don't want to use it, in which case there aren't any relevant settings to be lost. Either way, I believe the settings you may or may not need are preserved when the plugin is disabled.