The transmission-daemon package from EPEL makes it easy to setup a command line bittorrent client on RHEL 6 or CentOS 6. However, I have encountered situations where modified settings in /var/lib/transmission/.config/transmission/settings.json revert back to their defaults upon starting the transmission-daemon service.
In particular, the rpc-authentication-required parameter will always revert back to false if set to true when using a default transmission-daemon install. This occurs because of certain switches being passed by the transmission-daemon init script found at /etc/init.d/transmission-daemon.
The particular line in /etc/init.d/transmission-daemon that is overriding certain parameters in /var/lib/transmission/.config/transmission/settings.json is the following:
DAEMON_ARGS="-T --blocklist -g $TRANSMISSION_HOME/.config/transmission"
The -T switch causes transmission-daemon to never require authentication, and the --blocklist switch enables peer blocklists. If you would rather your settings only be defined in /var/lib/transmission/.config/transmission/settings.json, remove those switches. I would suggest copying this line, commenting it out, pasting a new line, and removing the switches from the new line in case you ever want to revert to the default settings. The new DAEMON_ARGS line would then look like the following:
Now, all settings will only be defined in /var/lib/transmission/.config/transmission/settings.json.
Take note, in order to change any settings in /var/lib/transmission/.config/transmission/settings.json, the transmission-daemon service must be stopped. Changes made while the service is running will be ignored and set back to their previous settings upon restart.