Simple. I never did pick up that scroll, so I never went to her lair, I just progressed with the game without searching for Evelyn, assuming that she and the doctor left the town because they noticed that I am on their tracks.
The game reacts to that with the Doctor proceeding with his plans, when you finally met him, Jack was able to free himself and arrives at the place as well. Jack than tells you that Evelyn underestimated him, etc
Quite logical progression of the game if you ignore Evelyn. As it was mentioned from many people, you do not need the amulet from her, because all other high-ranking members of the cult have the same amuletts.
