After you replace the licence.xml in the WEB-INF file, you should be able to start teaming and reload the license without having to run the installer in reconfigure mode

As an alternative, if you want to use the installer in reconfigure mode, make sure the new license is in the same folder as the installer with the name license-key.xml, the installer will copy this file and replace the license.xml file in the WEB-INF folder

If you replace the license.xml in the WEB-INF folder only and run the installer in reconfigure mode it will take the license file it has in the installer folder (I assme the old one) and replace the new license in the WEB-INF folder, which might explain what you are seeing