While the configuration files used by the SQDaemon are not frequently modified for either Capture or Engine Controller daemons, they will from time to time be modified for example if another Engine or Capture/Publisher will now be managed by the same daemon.
On all platforms, (zOS, linux, AIX, Windows), changes made to the SQDaemon Agent Configuration FIle are not effective until the daemon is either restarted to it is refreshed using the SQDMON utility with the "reload" parameter or the task simply restarted. In particular the Authorized Key List File must contain the Public Key of any Engine agent that will be remotely connecting to the daemon. On zOS, there is a shared ENQ on the Authorized Key List dataset by the daemon started task, so you can't update it from another address space (TSO or batch) because that requires an exclusive ENQ.
There is however no harm in stopping the daemon long enough to update the auth keys file, then fire it back up again. The worst that could happen is that it would miss an incoming connection during the time it was down.
One option is to copy the existing Authorized Key List File to another file, update the other file, then stop the daemon, rename the files, and start the daemon. Daemon is down for maybe 15 seconds.