The cache is used by the jvm to store the required files locally. Think of it as system files. I do not think allowing the user to edit something in the system files is a good idea. You can probably provide a UI in your application to edit them.
What exactly do these files contain? Some editable properties? If yes, then you can access them using System.getProperty() Take a look at this
thread https://coderanch.com/t/200507/JNLP-Web-Start/java/JWS-properties-file
If it contains something more complicated than properties (name value pairs) you can
probably treat them as resources. (Note: I have not tried this out myself) More on resources here
http://java.sun.com/j2se/1.5.0/docs/guide/javaws/developersguide/syntax.html#resources
Another way (more elegant in my opinion) would be to store them on the server. Since you are using JWS, you can get/send this data from the server. If your application has multiple users, you will of course need to map these to the user.
Another option might be using the
Java Preference API
Of course I am just thinking out loud here as I really don't know much about your application and requirement.