What I've noticed is that new versions of Java have their own cache directory. All my settings are safe, but I have to go back to the updater Web page and re-run the application from there and tell it to recreate the desktop icon. Re-running it causes it to get read into the cache again, and recreating the icon makes an icon that points to the right spot in the right cache directory.
I think adding a new version of Java doesn't break anything, but an update that replaces an old version (deleting it from the system so only the new version appears) breaks things. The automatic updates always seem particularly problematic, I switched to manual updating to make sure I got 32- and 64-bit versions in the right order.
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