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I have four VM's running on a Windows Server 2008 R2 box - not 'core.' What is the best way to install Windows Updates on that server? Do I need to shut the VM's down first in case it wants a reboot? Is there a way to configure Windows Updates to do the shutdown itself?

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WIndows saves the VM's then restarts. If saving takes too long some vm's just fail and restart from cold boot.

Server 8 can - in a cluster - empty the machine by moving the VM's over first, but that is not in standard 2008 R2, sadly.

We do save / shutdown before upating the virtual servers. But we only have three.

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I did an experiment this morning as I ran updates on the VM host server. I paused & took snapshots of all the VM's before rebooting. When the server came back up all the VM's woke up too with no ill effects. – n8wrl Mar 17 '12 at 13:44
Small? I have al arger server and we sometimes get a rese here and there - possibly a timeout saving all the vm's. – TomTom Mar 17 '12 at 16:46
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Assuming that you are working in a Hyper-V cluster you'll want to manually move all the guests from the host to another host then patch the host.

If you are in a standalone config you'll want to down the guests then patch the server.

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