First, a bit of business: you may not have read our naming policy on the way in. It requires that you use a full, real (sounding) first and last name for your display name. Joke names and "handles" aren't enough. You can change your display name here. Thanks!
Now, as to your question: a qualified "yes". If your changes don't break anything, then yes, this is fine. But if there are digital signatures in the jar file, this may break them; and of course, arbitrary changes (like replacing a class file with a grocery list) will likely break the application.