This plugin will automatically set and/or update the Authenication Unique Keys in the wp-config.php file.
No, every other line does not get touched.
The plugin will display the values for you to manually update the wp-config.php file, using FTP or whatever method is allowed by your webhost.
The plugin will generate a new set of keys. The only thing it does is log you out temporarily. By updating the keys on occassion, provides more security for WordPress.