Had the same problem. Decided to destroy the codex and was told to return to the tenebous ship to speak to keeper (minister). When I got to the airlock to get onboard, the doorway was red and i couldn't enter. Sent a ticket and the dev basically told me that he had reset my quest and that the option to destroy the codex wast the problem and that I HAD to pick one of the others. Can't be neutral. About to finish this thing one more time. Hopefully it won't bug out on me again. GL with yours!