No, no, no.
You don't "go back" to the Java code to modify it. You simply debug, test and modify the Java code. You ignore the code in the compiled javascript files except to deploy it. As far as you are concerned, GWT source code is Java code, not javascript, written within the environmental restriction of the browser.
Your question is like asking, "I have a C application that gets compiled to object code. Do I modify the object code or go back to the C code to modify it?" !!!
You simply treat the generated javascript as "native code".
No doubt you can include javascript using jsni, and so can you include assembly code when using C. So except for those assembly code you inject and similarly except the javascript code you include, you leave the "native code" alone.
When you try to modify the object code generated from C, that is called hacking. Hacking is an interesting hobby but when you wish to create an application and your main task is not "hacking", hacking would only be your extra-curricular activity not connected to your main employment or project.