Source files missing after wsus install

2 days ago I decided to install WSUS and SUP on our SCCM 2012 server and all was going good until this am when I discovered the folder that I keep all of my software deployment in under the sourcefiles share was empty. I did take a snapshot
of the server before I started the install and everything seemed to go well, I could see my updates and it was syncing fine. Now if I boot the server normally the folders disappear under \sourcefiles\applications. If I boot to the snapshot they are there but
after a while they disappear as well and the updates show up under software updates without the wsus role installed on the server. I can see the folder right now and I am copying the contents to an external drive. I had setup windows server backup to back
up my whole hyper-v server sccm and sql are on the same box but I could not get backups to open at all, so this snapshot and the one I did when we did the initial install are all that I have. I have the sourcefiles shared out and mapped to my desktop and the
size of the share keeps changing as well.

I'M pretty sure I had WSUS configured right, I have a lab at my house and it is working fine although it is on Sever 2008 and is 3.0 not 4.0. I have made some progress today, I found this blog about SCCM 2012 and WSUS last night which really helped. I removed
WSUS this morning and the updates were still there but if I read the article correctly it says they will remain in sccm for 7 days when they are "tombstoned" so we will see. I am running a scheduled sync right now and it's almost done but I have also created
a folder under software updates and moved all of the files there. During my sync I have been doing a search on that folder for expired "no" and selecting all and moving them back to the root folder.
http://blogs.technet.com/b/configmgrteam/archive/2012/04/12/software-update-content-cleanup-in-system-center-2012-configuration-manager.aspx
Anyway thanks for your help

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