You can use a helper application: Start it using a java -jar updatehelper.jar call, then quit your main application. There are many tricks to get around this problem: I don't know about MacOS, but I think this approach is to weak to even try it.
On Linux, overwriting possible, but because Java doesn't copy the whole file into RAM, it can happen that your code fails at some stage because it isn't possible anymore to load new classes from the file (this is likely to happen for example for a class AskShutdownDialog which will only by used at shutdown). I guess you have a problem with overwriting the file while it is currently in use? This heavily depends on the operating system: On Windows, Java locks all jar files which are currently in use, so overwriting is not possible.
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