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I subscribe to a provider than gives me a virtual private server running Windows Server 2008 R2, from which I host several low-traffic websites. Currently, Windows Update runs automatically on this box and once in a while I will log on and see that it has been restarted because of updates having been applied.

Like I said, the sites are relatively low-traffic, but I'd hate to have the site become unavailable in the middle of someone's session.

I realize that there are ways to disable both the automatic updates and the reboot, but I'm curious:
Is there any intelligent checking for active connections or IIS idle time before forcing the system to restart?

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Not by default, no. It will reboot once that timer expires regardless of what is happening on the server at the time.

This is why having a strict update policy is a must for public facing servers (and also for real-time servers like SQL and RDS/Terminal Services).

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