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We too have HA configured. When I first got involved with Control-M two years ago, I did the manual service stops and server reboots as this is what I had been told we need to do. I have had this same conversation with BMC support and was told that we did not have to stop the services or reboot the servers in any special order. Our next patching cycle, I let it run automatically including the server restarts and all went well. The only thing I did was stop the services on our HA server since I did not want it to be primary. It patches in a later patching window. What we have since done is set up a Control-M job to stop the HA services prior to the automatic patching window and to put our servers in maintenance mode in our enterprise monitoring system (Zabbix). Now we do nothing for our automated patching that occurs Sunday morning. We have mostly safeguarded this window from having jobs scheduled in Control-M as this is our standard maintenance window for the majority of our systems.
Hope this helps.
We have our primary and secondary servers in different patching windows at least 1 week apart (the servers are on different VM infrastructure at different sites, including MSSQL cluster setup).
We fail over to secondary prior to our primary patching, then we fallback to primary prior to our secondary patching. This way if the patching introduces any issues on the primary system we can run from secondary and delay the secondary patching until the issue is resolved.
It also means we don't get called at 4am to PVT Control-M