That part of the instructions is a bit misleading. You can actually disable or wipe the Java temporary files after you installed it and it will still work fine, but it will put considerable more load on Kaldran's server since the updater would be downloaded every time you run it. The updater is a Java Web Start application, meaning that it is designed to be run transparently from the web, but unless something was changed at the source it can run from a local cache (the Java temporary files). You can try wiping your cache manually and you will see that the updater will still run fine.
That is because it is in fact "permanently" installed, there is even an entry in Windows' add/remove software panel, but apparently (from what you describe) your third party software is ignoring this and wiping the updater installation regardless. So that's why I consider the software "broken". I don't know that software, but maybe you can teach it to ignore the updater.
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