Yep, I found this bug on my first long rest after patch 1 too. I haven't actually progressed Raphael's quest yet, beyond ...

turning down his deal as is still clearly stated in my journal. I've not yet been to the House of Hope.

I've sent a bug report to Larian and I assume others have, too, so hopefully it'll be fixed. I'm just ploughing on regardless, so if I find that it has any downstream consequences I'll update here.

"You may call it 'nonsense' if you like, but I've heard nonsense, compared with which that would be as sensible as a dictionary!"