See the Deployment wiki - Upgrade Troubleshooting section entitled "Licenses" which provides a variety of information on licenses during the upgrade process. https://jazz.net/wiki/bin/view/Deployment/Licenses

Essentially, the licenses cannot be upgraded. You need to import new 4.x licenses which will overwrite the 3.x ones. If you have purchased 3.x licenses, you are entitled to 4.x licenses which can be downloaded from your Passport Advantage site.