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My experience is that depending in which java version is being updated the applications installed in the previous version dissappear and they have to be installed again. I had a similar problem ( i think updating from java 6 to java 7) and at some point I read the whole release notes of the update and they said that older versions would be uninstalled. And with the older versions the application installed with those older versions. Result: A new java version and the applications gone.
That's useful info thanks. Another hiccup I have discovered is in cases where the jnlp file specifies that the program should have a menu option as well as a desktop icon (as mine does). If the end user deletes the icon, but not the menu option, the Java mistakenly believes the desktop icon is still present. So in the control panel, the button to create the desktop icon remains greyed out.