From my requirements:
Your programs must not require use of command line property specifications. All configuration must be done via a GUI, and must be persistent between runs of the program.
So no, you can't require the user to edit any property files manually. BUt, the way you describe it, you already have a dialog for the Server... all you have to do is open it every time the server starts. Display all the values from the property file. The user can just press start, or he can change them first and then press start.
I was going to write a full GUI for the server, but I think I actually like this approach more because in the future, it is easy for the app to bypass the dialog and behave like a "proper" server app