The best way to upgrade the WebManager is to run the new version in parallel with the current application, then run 'Synchronize' from the new version, and finally point users to the new version. This has the benefit of leaving the current production WebManager untouched during the upgrade, allowing the administrator to direct users to the new install only after it has been properly tested, with the old install available for instant reversion if necessary.
Rename the WAR containing the new version of JWM to a name which will not conflict with the current application. For example, if the current Web Manager is running in the servlet container at '[web app root]/swm/' folder (having been unpacked from 'swm.war'), then rename the new 'swm.war' to 'swmA.war' or any other suitable name. In Tomcat, just place the new WAR in the 'webapps' directory and it will unpack into the '/swmA' directory. For other servlet containers consult your documentation about adding web applications to the context. The goal of this step is to have two Web Managers running side by side at '/swm' and '/swmA'.
Go to the command line of the OS and navigate to the newly installed Web Manager root (swmA). There will be a 'run.bat' file for Windows, and a 'run.sh' file for Unix/Linux. Execute the file appropriate for your OS. If you are unsure of how to do this, please consult a knowledgeable system administrator within your organization.
This will run the Web Manager in command line mode. Type 'y' and Enter to accept the default directory. Once Web Manager is loaded and the blank 'WebManager%>' prompt appears, type 'synch();' and Enter to start the synchronize routine. Follow the instructions, pointing to the old install ('swm') as the 'source' server. This routine will pull over user, group and session data and configuration files. Now both Web Manager installs should be roughly equivalent in the data they contain. Test the new Web Manager to be sure it is properly configured.
Finally, use whatever features your servlet container provides to redirect users to the new install. In Tomcat, simply stop Tomcat, rename 'swm' to 'swm_old' then rename 'swmA' to 'swm' and restart Tomcat. Now users will reach the new installation of Web Manager. Consult your servlet container's documentation. The benefit of this technique is that now the 'old' version is still available and running if for some reason you should need to switch back to it.