We have a lot of long-lived processes, of which hundreds are "running" at any point in time. That's why we planned to do an in-place upgrade.
On a JEE install, seems like it is a fresh install. I create a new install directory, creates new EAR files, and then the Configuration Manager knows it's an upgrade from the selected version. It upgrades the Repository and keeps the "running" processes in tact.
Seems to go along with what the upgrading documentation was saying. Does this not work in the real world?