Just a suggestion,
You could make the new Version Jar's update to a separate folder each time and have the local settings/global settings save to that version folder. When launched a prompt would come up allowing a person to access the current version or a previous version.. and also allow them to delete old versions if not required any more.
That would save you the headache of handling multiple installs, and keep different setting files for each version.
if your looking for a beta tester wink wink
edited
Also your version checks would compare against the latest version the users system.