I recently needed to move the WSUS server that was synced with Config Manager. The first time I attempted to move WSUS to the new server I didn’t factor in that SCUP was also synced with WSUS/ConfigMgr and this resulted in some configuration errors in attempting to setup the new WSUS server when installing the software update point.
The SMS_WSUS_Configuration_Manager Component status giving me a 6603 error
Opened up the WCM.log to find this error : Failed to set Subscriptions on the WSUS Server. Error:(-2147467259)Unspecified error
as you can see a few lines before this error, we are getting a log of Category Product (System center 2012 Configuration Manager ) not found on WSUS. This told me that there was something in the ConfigMgr database that was looking for a ConfigMgr update to sync still with WSUS. I attempted to setup SCUP and republish the ConfigMgr Updates but this didn’t fix the problem due to the Unique Update ID not matching I believe. Luckily I had the old WSUS server still up and running so I added the software update point back to the old WSUS server and found that I had missed unchecking the Configuration Manager updates from the product tab. (I forgot to screenshot at the time, but here is where you would find the additional products that need to be unchecked)
Once you have unchecked the products published by SCUP watch the WCM.log for the configuration changes to be published to the WSUS server and then it is safe to removed the software update point from the old WSUS Server and proceed with setting up your new WSUS/Software update point.
I have also seen issues when you have products selected that WSUS is not aware of until after the initial sync with Microsoft Update. Best bet is to ensure you have unselected all products and classifications before attempting to remove your last software update point in a site to ensure a pain free addition of a new WSUS Server.