So to explain the whole situation, I need to start from almost the beginning. When I first got to the Cyseal, I spoke to everyone I could before venturing off into the wilds. When I met up with Evelyn, and found out about that little side quest with Boris and Steve and how you could only save one, I reverted to an earlier save and kept from talking to her at all in hopes of finding a way to save both.
I went and investigated the crime scene and got the letter to show to Esmerelda, but halted the Councillor's Wife quest there. I dug up Jake's body, spoke to his dog, and interrogated Roberts before stopping the Mysterious Murder quest there.
The urge to explore the map got the better of me and I left Cyseal to see what else was in store. Long story short, I found Dietmar and his thugs and a journal entry appeared in the Mysterious Murder questline saying something along the lines of "We found the path to Evelyn's lair mentioned in her diary but had to fight past Dietmar and his thugs" and the quest was then labelled "completed". I thought it was just a little hiccup at the time and just disregarded it, even though I hadn't spoken to Evelyn yet nor acquired her diary.
I explored the map some more and found the Undertaker's Hut, broke down the door, and found the documents stating Thelyron and Evelyn's involvement in the undead plaguing Cyseal. When I went back to Cyseal to confront them, they were both gone. I figured that perhaps I would meet them again later on in the story.
I continued along, found the barrier that needs the enlightened amulet and saw that I didn't have it. I assumed Evelyn and Thelyron were behind there and that I would find the amulet later on. I made it Silverglen, took down the purple barrier around the White Witch's cabin, fought and killed Vaelenna, and found the enlightened amulet from one of the Immaculates around her.
I went back the barrier needing the amulet to find a dying Thelyron and an invisible (is he supposed to be visible?) zombie Jake speaking to me, praising the fact the Evelyn is dead (by my hand I assume). I killed King Braccus and and reported back to Captain Aureus and that's where I am right now.
When I try to continue on the Councillor's Wife questline, even with the knife and murder book in hand, all Esmerelda says is she can't believe Jake was a Sourcerer. She doesn't say anything about investigating Evelyn. I don't really know what to do. I feel like I've screwed myself out of a lot of content because of the path I took. Any advice?