Hello,
at the momenta every plugin which needs some configuraiton uses its own "config.php" file. This file is overwritten by updating the plugin over webinterface. It would be great to not loose any config files.
Maybe you could create a backup archive of the plugin before updating it and store it inside a subfolder. So the admin is able to switch to any previouse version or to extract the config files if he forgot to backup it (and maybe to restore plugins or the config file from webinterface).