I managed to get corporation cooperation prior to getting to the archive, with the order agreeing to take the Archive but allow Aunty access to some materials.  Secured Spireton with the help of both Order and Aunties troops, gave the calcedeceus(?) to the Order NPC who greeted me after fixing up the Archive, and patted myself on the back for a job well done. Then I head back to Ruth to tell her of my achievements and she acts like she's never met me before, demands I hand over the calcedeceus (which I shouldn't have in my possession), after which I find myself with a shoot on sight status with AC. Can anyone shed any light on this? I've had the dialogue reset issue with other NPCs and companions, but not to the point it ruins the outcome of the game.. please help. I've researched and I've done everything to enable cooperation and keep on both factions good sides, including good reputation 

Have you spoken to Vicar Levin?  I think that this is an important part of the quest, and the issue tracker says that this has been resolved (that is, if you don't speak to him, it borks up the quest), but I've seen several people having similar issues and I'm wondering if it *hasn't* been fixed, or if the patch only works for certain platforms.

I did talk to the vicar to agree to help negotiate peace, but this is another one of the conversations where I had the dialogue reset issue the 2nd time we speak with him, I wonder if that might be one of the issues..

Right. You talk to him the first time during the quest to help out with the negotiations. But after that (depending on what you did, and whether or not the delegates survived), when you go to Laplace's Garden on Cloister, he's there, and ideally, you speak with him before you meet Ruth for the first time. I missed speaking with him, but when I went to go meet Ruth initially, he was standing outside the doorway to her main space (the room with the sensory deprivation chamber in it); when I spoke to him there, he mentioned that he'd wanted to speak to me before "...but no matter" and I didn't experience the problem where Ruth forgets that she's already met you, etc.

I've seen other people reporting issues with this quest and there's an actual issue for this here: https://outerworlds2.obsidian.net/issue-tracker#k3VX6b0a-if-you-try-to-do-the-quest-an-equitable-arrangement-without-speaking-to-vicar-laureate-alden-levin-you-may-get-stuck-ar-126703 -- this was supposed to have been fixed in patch 1.0.6.0. Though if it's still happening for people (that is, if the actual problem is that progression is broken if you don't speak to Levin before meeting Ruth the first time), it might either still be broken, or maybe it's still broken for specific platforms.