Assuming it was the Ancients who turned off the Knossos of course.... 
The Shivans presumably understand the tech too and might have had their own reasons for turning it off. We know that they can get into GTVA space by some other route anyway.
Well, that idea adheres to my own theory that the Lucifer fleet was trapped on the wrong side of the Knossos when the Ancients deactivated it when they tried to consolidate their losses and isolate themselves from endless tide of Shivans driving them back. But unfortunately for the ancients, they still couldn't stop them. Why else would the Shivans have disappeared for so long? Only to return when the Knossos was reactivated and the figurative gate to hell opened anew.
As such the Lucifer didn't come into GTVA space via another route, it was simply in the neighbourhood having been trapped here for so long. Hence the lack of beams, etcetera on most of the ships save the flagship.
Unforunately, that idea kinda screws up my own campaign idea and I haven't been able to rework the ending without being a repeat of the old
