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If I run a Master SUS Server, what happens if it goes down? Should I build a backup server, and if so, how do I get all the clients to point to it?
Yes, it's a good idea to create a secondary server if you are concerned with high availability. Depending on how you are currently modifying the Automatic Updates component on the workstations, you will need to devise a process for updating the server those computers point to. Active Directory Group Policy is, of course, the easiest way to accomplish this, but it can be done through scripts placed in the login scripts. The
Microsoft Guide to Security Patch Management
gives details on how to set up a secondary SUS server and contains the information for configuring the scenario you are facing.