Thomas never presented his Engineering dialog option, so I ended up choosing the option where I tell him he should tell everyone the truth. Now it appears I'm unable to begin the quest. I have more than enough engineering (32 base), and now I no longer have a save from before I spoke to him. Is there another way to initiate the quest?

Hey, themaster24

I'm sorry for the quest issue you have run into. We have our development team looking into it and hope to have a fix for it shortly. In the meantime, to expedite your request, you can send an e-mail to our publisher, Private Division at support@privatedivision.com. This will get your issue into their queue and allow us to prioritize requests to ensure the fastest possible turn around time.

We apologize again and thank you for your patience while we work to resolve the issue.