Hm, the Pokeballs are designed for the Pokemon's comfort, trapping it in there wouldn't be wise for a normal trainer. It would be angry. Professor Oak may have a different storage mechanism in those black Pokeballs, in order to keep the troublesome ones contained.

I don't know how that would be possible. Removal of the ability would require knowledge of how it works, wouldn't it? Can you make a pokemon forget how it does things?