[1.3 Ideo] Defeated Factions showing up as required allies in Archonexus Quest

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On the third colony of the archonexus questline, it's now told me that I need to ally myself with a faction i completely defeated two colonies ago.

I would expect the quest to choose a living faction, or revive the dead faction (imo, this is the worst solution), or summon a new faction.

(As an aside, there should be an alternative if you it's too difficult to ally with the faction, due too ideologies some factions can have a strong dislike of you, and one of the easiest ways to make them happy is raiding other factions (now you've gone full circle and defeated another faction that might cause the issue).

To recreate the issue, defeat all the factions, except the one needed to complete an archonexus quest. After you move to the new colony you will receive a new quest requiring you to ally with a defeated faction.

This issue is magnified by mods like little planet, srts expanded and other mods that make global travel easier.