Over the years, I've always made a habit of uninstalling the old server version, manually deleting the folders and other junk that the uninstaller missed (except for my data. of course), and then installing the new server version.
The ONLY time it bit me was when I upgraded the Traveler server this last time - uninstalling Traveler also deleted the Traveler database files! That was a surprise. Fortunately I had copied them - and I don't know why....
;-)