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When you upgrade a Microsoft Windows Server Update Services (WSUS) server hierarchy to WSUS 3.0 from the top down, you must run the IISReset utility on the upstream server (USS) after you run the cleanup wizard. IISReset refreshes the Web cache to make sure that downstream servers can continue to synchronize from the upstream server.
In the following scenario, a failed synchronization may occur on a downstream server that is not yet upgraded to WSUS 3.0:
You install the original release version of WSUS 3.0.
You set up a server hierarchy that includes an upstream server and one or more downstream servers.
An upstream server has an update that includes more than one revision.
A downstream server has not synchronized the latest version of this update with the earlier version of this update.
You run the cleanup wizard on the upstream server.
You start a synchronization from the downstream server.