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.