I was going to play Spiral Knights, but when I clicked on the shortcut, it said the file didn't exist. I looked around on my computer, and found that Spiral Knights had uninstalled itself completely without my knowing. I do not use Steam. I just downloaded a Java update. When I tried to download it again, it said the file already existed, but I downloaded the game again anyway. It works.
I've had it too. It deletes the java folder thing and creates the new one — which the desktop launcher hasn't been set to the new one.
HOWEVER, you can still run the game with the web client. (Though I refuse to do that so I uninstalled and downloaded the game instead.)