Finally found out what was making the Knossos blow up. It appears right in the middle of debris and that takes out all of its health. But with the magic of invunerability, that problem is done.
And in my replaying of JAD2, I found a few things I should've fixed, and did so. So call it... JAD2.1 or something.
If you are in the process of playing JAD2 right now, in theory, replacing the vp should work. I didn't touch the campaign file or the names of the missions.