Skul's transmutation involves turning himself into an indestructible (by verse standards) statue. He can't move, can't think, and doesn't know whether he'll turn back to human in a few minutes or a few decades.
Bodily possession? Skul resists both mind and soul hax. Unless it works by telekinetically making his body move around or something, I doubt that's flying.
I dislike arguing on my own threads, but I'm also like the only person on this wiki who knows Skulduggery Pleasant, so ...
His elemental manipulation lets him do a few things. He can control air to mimic telekinesis or create forcefields. He can throw fireballs and shoot flames like a flamethrower. He can manipulate water or moisture in the air, making things wetter or drying. He can cause small tremors in the ground (not really useful here) or manipulate the earth to pass through it and reform it behind him. And turn himself into a statue of course.
Mind Manipulation lets him issue simple commands to people if he knows their given name, though having a taken name negates that, and considering how many names Flagg's had, that isn't flying.
If he gets pissed off / desperate enough he can release a shockwave of darkness from his chest capable of shattering all the bones in
the Black Cleaver's body, though he wouldn't do that willingly, it would just happen on instinct. However, once the darkness is out, he can control what it does.
Invisbility orb basically projects a small one metre or so radius aura around itself that makes anybody inside invisible.
Handcuffs make the wearer unable to use magic, so if he snaps them on Flagg's wrists he'll negate his powers.
Skulduggery's clothing is all made of physically and magically resistant materials.
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