What you can do to clean your SoftwareUpdateServer (SUS) is:
Use these steps to remove the older updates:
1. Open Server Admin.
2. Stop the Software Update service.
3. Click the Settings tab.
4. The storage directory for your software updates is listed next to "Store updates in:". Locate this folder in the Finder.
5. Delete the folder named "html" inside it. You will need to use the sudo command or enter an administrator password in the Finder.
6. Start the Software Update service in Server Admin.
(taken from Article: HT5198, March 22th, 2012)
After restart SUS, your Server will download all the Updates again. The content of the folder of my server is around 50-60GB!
ClamAV is preinstalled with MacOSX Server. It is a virus-scanning software.
OK, maybe you want to reset your SUS?
1. Verify it's not trying to do a sync by launching activity monitor and selecting all processes and type sync in the Filter field, nothing should be listed if it's not trying to update
2. Stop the SUS Service
3.Remove the following files from the server:
(In order to view the contents of hidden directories such as /etc, use the Go -> Go to Folder Menu Item in Finder.)
/etc/swupd/swupd.conf DO NOT DELETE
/etc/swupd/swupd.plist DO NOT DELETE
The contents of /var/db/swupd/html ( DO NOT delete this folder, only the contents )
Alternative, if you prefer to use the Terminal:
sudo rm /etc/swupd/.last_run
sudo rm /etc/swupd/.start_time
sudo rm /etc/swupd/.sync_done
sudo rm /etc/swupd/com.apple.server.swupdate.plist
sudo rm /etc/swupd/com.apple.server.swupdate.plist.previous
sudo rm /etc/swupd/swupd.plist
sudo rm -R /var/db/swupd/html
4. Restart the server
5. Once the reboot has taken place, use ServerAdmin to re-configure and start the Software Update Service. Allow the server time to re-download the software updates (this could take anywhere from 3-30 hours depending on connection speed of the server). Wait until it is finished (watch the log!)
6. Test Client update against server.
Hope this helps,