There seems to be an issue with one of the missions. I finished the mission that was recieved right after Finding (NPC), and it put me in an "endgame" cutscene. After that I tried to load a previous save to a point before Finding (NPC) but the mission list and npc's remained as if I had completed those missions. I probably have to start a new game for a clean slate.
After finishing Finding Kara, I was able to go to the basement and do the abbess's bossfight. After completing it, it immediately showed me the cutscene with Kara, Therese, and Magda, after that I got the mission, Kill Reignvoldt. At this point most of the Cathedral (aside from Magda's path) was still inaccessible. However after reaching the Cathedral, a cutscene played and skipped me to the Angel boss fight. At that point I tried to load a previous save from before Finding Kara, but when I did the game was still in a state where Kill Reignvoldt was active. Kara and Therese were not in their usual places, and I wasn't able to access Olivina as an NPCs.