In one trailer, Batman visibly hesitates a punch, like he's resisting the mind control. I mean, it makes sense since he's fought Scarecrow, Mad Hatter and Joker in his mind multiple times now.
Anyway, with continuity regarding the movie and comics, my personal views is to not worry about it. This is comics, we can literally create an explanation for anything. Regeneration, alternate timelines, alternate universes, clones, identical twins, it doesn't really matter. I mean, Joker could literally come back to life and it wouldn't surprise me (don't do that though, lol).
Captain Boomerang was dead, now he's alive again. Enjoy your game.