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Another problem would be the file names and locations. If in the same folder the new jar would need a new name.

An idea: copy contents of current jar to a new jar(if that is possible??) and add the .ser file to the new jar. Then the tricky bit. Start that new jar executing with a ProcessBuilder/Desktop or ??...

There was a thread on one of the forums about a project to update a jar file. Take a look at this thread:
Help with manipulating files in a jar - Java
I'm not sure you would be able to update the...