They should have spun up a new server to act as secondary the moment replication failed. This new server is the one you run all of these commands on, and if you make a mistake you spin up a new one.
Only when the replication is back in good order do you go through and kill the servers you no longer need.
The procedure for setting up these new servers should be based on the same scripts that spin up new UAT servers for each release. You spin up a server that is a near copy of production and then do the upgrade to new software on that. Only when you've got a successful deployment do you kill the old UAT server. This way all of these processes are tested time and time again and you know exactly how long they'll take and iron out problems in the automation.