Now that we've had some more time to work out our narrative, and I've had more time to think on this, I've come up with the proposed sequence of events for the Cognis in the new timeline.
-Xander rises to prominence as he did before, one of the stasis-hoarded 'frost-born' used as bartering chips by the Xandrians. He successfully manipulates his way to have a and unknown significant access to resources so he can further pursue his own projects, emulating the successes of the Dark Age of Technology and Xandria's own forbidden past, without outside interference.
-Xandria encounters the Imperium, and Xander himself realises the edicts of what he considers a 'False Omnissiah' risks undermining and damaging his work. In-between the time a delegation is dispatched to meet the Imperials who have entered their territory and the return of that delegation with Imperial envoys, Xander has usurped control of the Forgeworld.
-Seeking a potentially pliable ally amongst the Legiones Astartes, xandria offers the services of his Forgeworld to the Primarch Socraes Travier, newly appointed to lead his Legion. At the same time he begins to cultivate allies among Forgeworlds whose members hold similar views to his own, bearing disdain for the edicts of Terra and Mars like. Covert trades are offered, military build ups are whispered of, and the nascent form of what is later known as the Cognis Heretica is born. On Xandria itself, the Archmagos uses his new resources to pursue his hidden desires to the full.
-Socraes Tarvier fall to chaos begins. Xander hears only whispers of the new revelations, but the idea of a whole avenue of research forbidden by the Emperor above all others proves intriguing to him. Slowly, he begins to turn away from the secrets of the Dark Age of Technology and towards even darker pursuits.
-The Emperor is lost and the Warmaster slain. Xander believes now is the time for rebellion, but is persuaded to hold of by Ixipatian, who whispers of greater rewards and opportunities yet to come. Despite his concern about how much the Primarch knew of his plans, Xander agrees to hold back.
-The first Inter-Astartes war begins. Despite their close ties to the Regenticist Eagle Warriors, the Xandrian Mechanicum quietly side against Mars and Terra, held again in the grip of a new tyrant, and with the rebels. So too do a number of isolationist and militant Forgeworlds, each of which is a member of the Cognis. The extended network of Explorator Fleets proves ideal for ferrying supplies to the rebels and raiding the more established regenticists, though at a mercenary price. Xander's true goal is to use the war as an excuse to militarise yet further and have the Space Marines bleed themselves against one another, a plan that fits all to well within the schemes of Ixipatian.
-In one of the last campaigns before the Regent's flight from Terra, the Regenticists launch an assault on Xandria, havinf identified it for the rebel supply hub it has been acting as. Xander is forewarned by Ixipatian, and as the battle commences begins to put his warp-theoreticals to the test. Ancient Xandrian projects, long forbidden and forgotten for the catastrophes they proved to be, tear their way from beneath their glacial plains now infused with the power of the warp. Foremost are the automata-Titan abominations now melded with daemons, an unholy abomination of metal, organic cortex and daemonic spite. One of Xandria's earliest projects, the Silica Animus known as Rapitarius, rejects an attempt to subject it to possession and successfully flees, taking it's overridden sub-Tagma with it. Xander will later attempt to build a replica with his new knowledge, but it will be a twisted shadow of what has come before.
-The Emperor is returned. No longer are there Regenticists and Rebels, but Loyalists and Traitors. With the return of the Golden Tyrant, any pretence of the Cognis' loyalty to their former allies is shattered.
-Insane, and utterly enamoured with Chaos, Xander begins his great work to build a new Legion of warriors from the Cognis and lead it to where the armies of the shattered Imperium converge to fight the war's final battle. As Terra is besieged, Xander hopes to plunder Mars and Terra alike, to destroy the lapdogs of the Emperor and above all to receive the ultimate illumination from Ixipatian, herald of the fourfold pantheon. Many follow him. Others let them. Though they would never serve under the Emperor again, there are those among the Cognis who are wary enough of chaos and yet another supreme tyrant to avoid rushing to their annihilation. It is these last embers that kept their armies close that will survive into the coming age.