When upgrading the RHQ server and keeping the database, we should try to read as many preferences as possible from the database. This would e.g. apply to the setting for the smtp server. In addition the installer should ask for the location of the old rhq-server.properties file and read the settings from there to server as preset for the upgrade. The installer should also try to copy over the license file. It should be able to determine its location from the path of the properties file above. Alternatively, it could just ask for the base directory of the old install and determine the paths from there.
This bug was previously known as http://jira.rhq-project.org/browse/RHQ-1898
rhqctl upgrade does this.