The configuration file is not modified by this command.
Persistent settings remain when the daemon is restarted.
Runtime settings are lost when the daemon is restarted. See section 3.8.2 on page for more details. It is generally wise to test a new configuration on a single machine to ensure you have no syntax or other errors in the configuration before you reconfigure many machines. Having bad syntax or invalid configuration settings is a fatal error for Condor daemons, and they will exit. Far better to discover such a problem on a single machine than to cause all the Condor daemons in your pool to exit.