I ran into a small issue upgrading to 3.2 and figured I would share in case anyone else runs into the same issue.
When you get to the point to click the Up arrow that upgrades your individual Viewer Applications, I ran into an error message which stated there was a HttpWebRequest_WebException_RemoteServer - Arguments:NotFound. After looking at the request in fiddler I found the message "The file 'C:\inetpub\wwwroot\Apps\PolicySearchTest\Config\Application.xml.bak' already exists."
So I looked in the Config folders of ALL my maps and found I had .bak files that may have been from the upgrade to 3.1 a while back. After renaming or deleting these files I was able to upgrade all my viewer applications.
Hope this helps someone.