I had a minor problem updating my Primary Server last night that I figured I'd share since I figured out the issue and fixed it manually.

In my case, for some reason, in the C:\Program Files\Novell\ZENworks\install\downloads\msi of my Windows Primary, I had files that were 10.1.2.msi and some that were 10.1.2.msi.superceded. The server upgrade will try to rename the 10.1.2.msi files to 10.1.2.msi.superceded. Since some of these already existed, the upgrade failed.

The manual fix was to go in and delete the extra files and redeploy the update.