Has anyone had any experience changing their application while the server
is running?  I'm looking to update my application (the jar file) without
having to reboot everything. This way clients stay connected, but I would
be able to update without losing them.

You can do this.

1. Make sure you that the jar files you need to update are loaded into
classpath using QuickServer from "application-jar-path" in XML and are not
in your startup/command line/boot classpath.
2. When server is running,  just replace the jar file.
3. Now invoke "restart server" using QSAdminServer (via telnet or shell or
QSAdminGUI)

The re-start will not kill connected clients. The connected client will
still continue to work under the old logic/classes. But when you now
connect the new client they will use new class from the jar that you just
updated.