Managed to complete the quest chain last night (after having PC issues). Abandoned quest yet again, and chose to hand over the item instead of destroying it. Not the option I wanted to use but at least its finished now.

Ive also had this issue when I have chosen to destroy the codex. When i return to the Tenebrous (spelling?) it says that I can not enter at this time. I raised a ticket and the response I got was that it was a bug and that it had been passed on to the developers and the ticket was closed. A week passed with no response so I tried resetting the quest and doing it again. Chose the same options and got the same result when I tried to return. I raised another ticket last night and got a live chat with a customer services rep. They said that the issue had been sent to the developers and that I would have to wait for a patch that would address the problem. They didnt say anything about a story option causing the issue. Going to try resetting it again and selecting a different option to see if I can complete it.