The question that always sticks in my mind is one that none of these non-canonical theories about the Shivans ever seems to address: Why did the Shivans wait 30 years to send a follow up force, and why didn't they reappear in the systems they first attacked? The Ancients believed they had trespassed, overstepped their bounds somehow. From the voice over narration, it doesn't sound as if the Shivans found them, but the other way around. Their empire was greater then the limits of known space, and yet most of the jump nodes (admittedly not ALL of them) that are not already known are too unstable for any but the masters of subspace travel (The Shivans). It seems patently obvious when the Knossos is first unveiled: This was the mechanism the Ancients used to stretch their empire across more worlds then man currently knows. The discovery of a second and then 3rd Knossos cements that.
Who knows how much further they extended before finally encountering the Shivans? And how could activating 1 Knossos device trigger countless others on the opposite side of a subspace portal, countless lightyears away? It makes much more sense to believe that when the Ancients retreated to their home system (GTVA space) they attempted to shut down the first knossos leading to the systems the Shivans came from.
Like the GTVA discovered, the jump node didn't instantly collapse, but had been stabilized. The Ancients wouldn't have any reason to know this ahead of time, after all, they were the masters of space, crushing all they encountered. Why collapse portals when you enter them in the certain knowledge of your superiority? And so the Shivans followed them, and all their works were undone.
So what does that have to do with the Lucifer and it's rather small battle group attacking the GTA and PVN 10,000 years later? The subspace portal in Gamma Draconis was no longer active. What the Ancients set out to do when they shut the device off was accomplished through time, effectively cutting off all the systems on the other side. Since the Shivans never seem to study the technology of other races, and since the gate was on the opposite side, they had no ability to follow. And yet there were still Shivans on this side of the node.
I surmise the Lucifer and it's fleet were somehow trapped, perhaps several lifetimes (or even longer) before. Shivans possess much greater knowledge of subspace travel and thus can use nodes too unstable for Terran or Vasudan craft, so the known galaxy for them would be quite a bit larger then it is for us, but still potentially cut off from the regions they came from. And so they wandered, who knows for how long, until they detected the subspace travel we generated and set out to destroy us.
I don't think the Shivans in Gamma Draconis had ever encountered humanity before, nor had the Lucifer's fleet been in contact with the rest of the Shivan race. Had they been, simply destroying the Lucifer should have triggered the sort of response the destruction of the SJ Sathanas generated (unless you think they built those in 30 years), and it would have been on their terms of engagement. They came through the node in Gamma Draconis and attacked us because we opened that door, and Shivans are attracted to significant subspace activity. Had Bosch not pursued his ultimately futile agenda, the GTVA might never have encountered the Shivans again.