One of the most common questions I’ve been asked is, “How do I remove SCUP updates from Configuration Manager?”. The answer is fairly easy, you expire the update in SCUP and the re-publish it into WSUS. Then on the next scheduled ConfigMgr/WSUS synchronization the update will be marked as expired in the ConfigMgr UI. Finally after a few weeks the update will be removed from the UI (unless the update is part of a deployment package).
Now this process becomes a little more work if you have deleted the update in SCUP and have no way of getting it back. One thing to remember is that the flow of data is one way, meaning it flows from SCUP to WSUS (through publishing) and from WSUS to ConfigMgr (through synchronization). If you publish an update to WSUS and then delete it from SCUP (before expiring/republishing) then the update will become orphaned in ConfigMgr and there is no easy way to remove it. If you are in this situation the below steps should help remove those orphaned updates.