I think this happened during or after "Here Lies the Abyss" (after the attack on the Warden stronghold/Fade adventure), and Blackwall is not there. His icon is there. Game dialogue indicates he's still around. But I go to the stables, and he is not there. Empty space where his icon says he is.
If it matters, I'm on PS3.
I've had some disappearing NPCs as well. I've had that happen with a few of the companions now and it's confusing. Save and reload and they'll be there.
Blackwall is missing for me too. Read multiple forums where people had the same issue but none of the bug-avoidance tricks are working for me - saving, teleporting across the hold and back, etc.
Cullen pulled this one when I got to skyhold for the first time. His icon was at the table at the base of the steps where he should be but he wasn't in sight. Save and reload didn't work, but I traveled to hinterlands and back and there he was.
I have the same issue with Vivienne in the skyhold. Reloading, restarting, etc. wont fix it. She's just gone. 
I've had a few companions go missing a few times (mostly Blackwall). Usually if I teleport somewhere else and then walk to the persons location they reappear.
Did manage to find him again! He was outside of the stables chopping wood. Though his icon didn't point there...
Did manage to find him again! He was outside of the stables chopping wood. Though his icon didn't point there...
I've run into that and that's very confusing. I'm glad he showed up for you though. 
I've noticed that alot of the characters for certain dialogue cut scenes that they move to different parts of Skyhold, but their indicators don't appears there, just where they usually are. I'd suggest looking around. Took me thirty minutes to find Blackwall at this same point and he was just outside chopping wood. Felt like an idiot.
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