Correct me if I'm wrong, the Lucy fleet entered from Ross 128, yes ? But the Knossos portal is at Gamma Draconis, or at least in its vicinity. That's quite a distance. And i doubt that deactivating the Knossos portal would've stopped the Lucy fleet from going home. Shivans can navigate unstable warp points after all. I also doubt that the Knossos Portal is precisely at the chokepoint of the universe. Its more likely that the Lucy fleet was a very old fleet that the Shivans thought would be enough to wipe out Earth, seeing as how flux beam weaponry was exclusive to the Lucifer itself.
Just because the Shivans can navigate unstable warp points doesn't mean they can navigate them all.
I don't think the Knossos is any sort of chokepoint, but maybe its node reaches farther than most.
As for Ross128, here's the timeline:
1. Shivans attack ancients
2. Lucifer fleet emerges from Knossos
3. Ancients turn off Knossos (or maybe, they turned it off before the Lucifer came through. Hoping it would stop them. But as you said, they can navigate unstable nodes . . . But after a while it became even less stable without the Knossos, such that even the Shivans couldn't navigate it.
4. Shivans destroy Ancients. Lucifer can't go back through Knossos
5. Thousands of Years pass; Lucifer wanders around
6. Terrans and Vasudans start to fight, the Lucifer which is not too far away, comes back to the general area, and is first seen in Ross128.
Thing about the Knossos is, we don't know where it leads. The Ancients built three Knossos in three consecutive systems. Why? That's a hell of an undertaking just to get to a nearby system. I think rather they stablized nodes which cover vast distances. Because really, such an investment in time and materials has to be worth it.
