Okay, let's assume for a moment that the nebula beyond Gamma Draconis was the result of a Shivan-triggered supernova. Let's also take into account Bosch's estimation that the supernova occurred 8,000 years prior to 'current events'. Finally, the last item for the table, the Ancients' destruction, also, 8,000 years prior to 'current events'.
How did the Second Knossos get in the nebula system if a supernova occurred there some time around the Ancients' demise? Give or take a few hundred years in between the events, I'm having trouble figuring out this little paradox and am surprised it hasn't been considered.
Case 1 involves the Knossos network already being established before the Shivan encounter. If this is the case, wouldn't the supernova caused by the Shivans have destroyed the jump gate? I'm certain that if three insignificant meson bombs could destroy the portal, a blast of a supernova would most certainly wipe it out, if it not cripple the device like the initial shockwave did to the Deimos and Moloch. Either way, that Knossos shouldn't work anymore if Case 1 is true.
Case 2 involves the Knossos network being established after the Shivan encounter and after the supernova. Now, if this seems probable to you, bear with me. The Ancients' view of the Shivans was that they were the almighty avenging horror of the cosmos. If they supernova'd the star in that now-dead system, what possible reason would the Ancients have for going back to that place. Even if they did want to make the Knossos network to explore what sort of Shivan activity was going on beyond the abyss, how would the ships survive the super-heated cloud? It takes centuries if not millenia for these nebulae to cool down. By that time, the Shivans have killed off the Ancients.
Case 3 involves the Shivans rebuilding the Knossos network, perhaps bringing in one of the devices from out of system. The problem with this Case is the Shivans themselves. Since when did they, for a xenocidal terror, use other species' technology? Sure, they travel via the Knossos devices, but I feel that's because they see the devices as jump nodes. It just so happens there's an old enemy's artifact making it possible, but the Shivans ignore that fact.
Case 4 proposes a whacky theory in which Bosch helps the Shivans build a Knossos from recovered pieces. This is whacky because it's... whacky. How would Bosch sneak the pieces through a GTVA secured node? How would this newly assembled Knossos stabilize a node that quickly anyways, while allowing enough time to call in the Sathanas Armada? Lastly, there's no evidence that is even remotely related to this theory... which is whacky.
Case 5 involves time loops. I won't explain as this isn't a real proposition for why the Second Knossos exists.