YES,you'd better run the WSUS Server Clean-up Wizard from the bottom of the WSUS hierarchy to the top and NEVER from the top down.
I totally disagree! The Server Cleanup Wizard should be run on the upstream server first, to ensure that
updates that will be deleted are no longer synchronized to the downstream server. Furthermore, if you run the SCW on the downstream server first, and it deletes updates that have had status changes on the upstream server that need to be replicated,
this may throw a synchronization error on the downstream server. The downstream server should NEVER be intentionally put in a configuration that makes it different from the upstream server, and running the SCW on a downstream server before running it on an
upstream server would do exactly that.
For more details on my thoughts about how to use the Server Cleanup Wizard in a replica environment, please view my webcast from Sep 2010
Using the WSUS Server Cleanup Wizard - Expert Tips and Tricks".