Defending Grit Gate bugged quest ending flag?

I'm in Role Play mode, and it was my fourth or fifth attempt to defend grit gate from the Templar. I beat the boss/ commander, but it seems like a second commander had spawned at the other entry point for some reason (don't think that was supposed to happen.) After I beat every Templar, the quest completed...- but the second commander (a wraith) was still alive AFTER the quest completion flag had set, and he killed most of my lovely bear friends (including apparently Q Girl...) I went over to quest giver's office in the southwest, and he told me only one bear friend died (which was true when the quest said it was completed) but I think no longer true at that point (though I can't say for sure who was/ wasn't dying to the wraith commander on the way over to the office)

With Q girl dead, the main quest seems to have become impossible to complete. The first step of the next quest after talking to Barithrum is to get the blueprints from Q-girl, but her corpse doesn't drop them (I'm assuming because she died before the quest was given) and the quest doesn't know she's dead (because when the completion flag set before she died)

This is as far as I've ever gotten in CoQ, and I'd love to be able to keep going- but it seems tragically borked at this point.

I understand this issue is pretty speculative on my part (as I just don't know how this interaction is coded or anything), but maybe there need to be more safeguards surrounding main quest flags/ item spawns for stuff like this... The quest should check if Q-Girl is alive when you speak to Barithrum, not just after Grit Gate is defended- even if this glitch hadn't happened, Q-girl could still easily die by standing in some plasma with low health in the aftermath of the Grit Gate battle or something- and if that happened I bet we'd be in the same situation where the quest doesn't know she died in the battle because she technically died right after it.

I'm assuming there is a backup plan in place already for what happens if Q-girl dies in the battle, but I guess I don't know that for sure... If there isn't, there should be, lol.

of course- the real issue is maybe that a second boss/commander Templar spawned to begin with (unless there are supposed to be two and I didn't realize?) I've encountered other spawn weirdness with saving/reloading in the past- but usually settlement checkpoint saves are pretty stable- so I'm surprised an issue like this happened.

Either way- I think my problem would have been avoided with a slightly different/more robust flag system surrounding the life and death of my bear friends in the defending Grit Gate quest.

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