Cleanup Thousands of old updates?

When in our Config Mgr Admin console:

Software Library > Software Updates > All Software Updates, we have over 10,000 visible updates.

I will also add that we have the HP Driver catalog and Patch My PC hooked into our SCCM environment.

Some of these updates are as old as 2011, Many/Most are Zero required.

We have WSUS processes we run monthly to clean up Expired Superceeded etc. We we run those processes which is a combination of the native WSUS cleanup, and some SQL and Powershell commands Microsoft gave us, it says its cleaning up thousand of Updates.

However we are seeing the same ones back in our WSUS a couple days later.

On our Primary SUP we have Superceedence rules set to 2 months, We have WSUS maintenance enabled.

What else can we do to clean up this environment and performance?