SCCM 2012 CU3 / WSUS - Update files are being deleted

We have been running this configuration since April of last year and haven't had any problems. 
The problem is a majority of the window/security updates files in the WSUSContent folder are missing.  I have ran wsusutil /reset and it takes a day or so but it will successfully download the 80GB of missing files.  But after a few days they are
once again missing.  We do run our EPP updates through WSUS and we have no problems with those.
I have searched endlessly through the log files, I can see where it goes through and skips them due to being superseded. 
Do not see any database or communication issues between SCCM and WSUS, per the wsyncmgr.log it sees the thousands of that are available from our WSUS server. 
So, any suggestions as to what might be causing the update files to be deleted from the WSUSContent folder?
We are running this on:
Server 2012 / SCCM 2012 CU3 / WSUS for 2012

So, just to make sure I understand.  Is that we should be deploying updates from the SCCM Configmgr? 
If you want to use the integrate experience, then yes.
but the problem is that a majority of updates are showing Downloaded = No when looking under All Software Updates
You need to either manually initiate the download of updates or set up an Automatic Deployment Rule (ADR). Either will cause ConfigMgr to download the updates placing them into an update package (which in turn gets placed on a DP where the clients can access
and download the updates).
wsynclog shows the sync of the update catalog, i.e., the metadata, and not the actual update binaries.
Jason | http://blog.configmgrftw.com

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