Lets say I am battling the inverse battle guy, I use thief on his Weavile and take his choice scarf. When the battles ends will my Pokemon still be holding the Choice Scarf?
You will steal the Trainer's Pokémon held item but you won't get to keep it permanently I'm afraid. However if you steal a wild Pokémon's held item you get to keep that permanently.
>Thief no longer steals a Trainer's Pokémon's items permanently; however, a wild Pokémon's item is still permanently stolen by the player.
No, From Gen V onwards You Cannot Steal a Trainer's Item Permanently. The only thing That Will Affect it Is It's Dark Typing
Source : Bulbapedia