I had never gotten around to finishing the second part of the White March in my earlier play throughs, so before I go fully into Deadfire, I wanted to have a character I could import who had, in fact, done all of the quests in the first game and its DLC. I reached the Abbey of the Fallen Moon and initially avoided meeting up with the High Abbot as I was playing a bit more of a frontal assault than a lie-my-way-in game. Through reading the Abbot's journal and everything else, I was able to do the Rising portion of the quest and get Ondra's device. I went to the Reliquary and met up with the High Abbot there, but I didn't have all of the answers to his questions, so I went to search the Abbey for the final answer. I walked into the central room of the Abbey (where I'd avoided being spotted before to skip that fight) only to discover the High Abbot there, and he was very angry at my presence. I was forced to kill him, so the quest updated that I'd have to figure out how to open the Reliquary myself. I went back up the stairs...only to be greeted by the High Abbot and his crowd again. After a few more rounds of question and answer, I ended up killing him again and proceeding.

 

This is probably not how this quest is supposed to work, right?

Various players fight and kill Kaoto in that Hall of the Tidal Wave without encountering him again in The Reliquary. So, based on your description I doubt something can be found out. Have you kept some savegame files before and after fighting Kaoto for the first time? Then uploading them to some public place is my suggestion, so developers may examine the files.

Various players fight and kill Kaoto in that Hall of the Tidal Wave without encountering him again in The Reliquary. So, based on your description I doubt something can be found out. Have you kept some savegame files before and after fighting Kaoto for the first time? Then uploading them to some public place is my suggestion, so developers may examine the files.

 

I'm sure had I opted to talk to/fight Kaoto in the Hall of the Tidal Wave prior to going down and drowning the Low Tide monks and retrieving Ondra's Witness, I would not have encountered him in both places. I do have a save from a little before my actions in the Halls of Silence and can recreate the situation. But for the developers, I'm not sure that's necessary. Understanding the steps I took should be enough to see where there's a missing flag for a potential situation.