The reason that I love this simple yet funny exchange between Batman and the Justice League is because Batman and Superman talking of two different things, sort of.
Superman is from the Earth before the Flashpoint Paradox occurred, so he’s not part of the rebooted continuity. He’s the actual Superman we all grew up with — at least in the comics. So Batman’s contingency plan he’s referring to are the plans that Ra’s al Ghul stole and used on the Justice League. All of this was covered in the Tower of Babel storyline in the JLA comics.
Batman, on the other hand, is talking about these briefcases he revealed to the New 52 Superman (the one who died and got replaced by Pre-Flashpoint Superman) during the Forever Evil event.
From – Justice League Vol. 3 #14