Congrats! You're the third person this week with a mysteriously disappearing or dying Halsin in Act 2, and about the fifth for the any NPC category!
All jokes aside, there's something majorly fishy afoot. There seems to be a 50/50 shot if an NPC will die or just disappear (or maybe they always die, but the game only realises they're dead in half the cases).
For my run, the first thing I did was trigger the Isobel fight. All possible NPCs survived (luckily), Halsin's quest went smoothly (I'm wowed), just for him to disappear after recruitment. I should theoretically be able to resurrect him at Whither's, but he doesn't seem to be dead. Bex is also gone. Maybe others I didn't notice, but those two for sure. Her husband doesn't act like she's dead. I do not even have Minthara. Something's got way worse in the Shadowlands during Patch 6... please debuff them, Larian!