I had the same issue. I cleared out Spireton before agreeing to help Auntie. I went back to Spireton and met their soldiers who said something like 'wow why'd you clear it out without us? oh well, we will take the credit' so it seemed like I was good anyways. When I used the console to activate the lifts, no one came up. I went back to the bottom and talked to them and I just have a [Leave] option and they still don't come back up.
I did not have high enough speech to do the truce and went with Auntie's Choice. I fixed the archive and resolved the personality conflict to all Yellow screens for Aunties Choice and talked to the Archive again and I can't interact with the Archive anymore. The "Recall Order for the Trifurcated Brain" objective still says "Secure the Archive for Auntie's Choice" "The Archive is badly damaged..." like the original post. When I went back to my ship, VAL told me about Horizon Point.
I figure this is all going to be bad endings anyways so I'll probably give up anyways.
