I'm thinking that perhaps Barnabas could have been in the course of making Quentin into a Leviathan follower when he was interrupted, and that the interruption inflicted damage to Quentin's mind, causing the amnesia.
How about when we find out the Book says never to kill people?!
The idea of its being in a lost language that only David Collins had the power to read was one of the cleverer twists of the story, I thought.