No their IQ became a singularity and sucked the Shivans in to GTA space.
I still think that the Lucifer was a rogue fleet.
Try this:
The remnants of the Ancients fled from Altair, they fled into a system beyond Ross 128, the node stabilized by a Knossos. They collapsed the Knossos after a covert group of Ancients within Ross 128 had disabled the Knossos, to prevent it from stabilizing the node.
(WARNING!! Really bad ASCII follows!!)
(covert Ancients) Ross 128 {Knossos}-----node-----{regular jump node} Other system (small fleet of Ancients)
(covert Ancients disable Knossos) Ross 128 {Knossos}-----node-----{regular jump node} Other system (small fleet of Ancients)
(covert Ancients) Ross 128 {disabled Knossos}-----node-----{regular jump node} Other system (small fleet of Ancients destroy node)
(covert Ancients) Ross 128 {disabled Knossos}/////node gone/////{Destroyed node} Other system (Ancients destroy node)
(covert Ancients die out/find others) Ross 128 {disabled Knossos}/////node gone/////{Destroyed node} Other system (Ancients move on)
(GTI enables Knossos) Ross 128 {disabled Knossos}/////node gone/////{Destroyed node} Other system (Shivans escape)
(Knossos is dest./de-activ./lost track of in Hades Reb.) Ross 128 {disabled Knossos}/////node gone/////{Destroyed node} Other system
EDIT: After leaving the system beyond Ross 128, the Ancients collapse the nodes to the system, thus sealing in the Shivans.