The docs for Java6 on javaws show that you can either use the executable to launch an app or to perform maintenance operations they call control options.
Two of those options are:
javaws -uninstall <jnlp>
javaws -import [import-options] <jnlp>
one of the things you can do is
javaws -import -silent -shortcut <jnlp>
So if you can run a script that first uninstalls your particular jnlp app and then silently re-imports it and its shortcuts then that would solve your problem. I don't think Java will automatically do this for you.
Note that the documentation says that it has to be a silent installation for the shortcut option to work. Also, I haven't double checked that this actually works myself.