Or they could just mean that the Batman in the JLA movie is a Batman further down the years as being Batman. It wouldn't be something that conflicts with Nolan's origin story cause they wouldn't be changing his beginning, just flash forwarding a bit into Batman's future. Thus, they don't step on the toes of Nolan's movies or mess with the superb beginnings of the character. Also, this would allow them to have another actor to play Batman with the excuse of them implying that Bruce Wayne is just older then what he was in the Nolan trilogy.
This sounds closer to what I understood from this article. IGN was the one to say "reboot," but in the actual article, "reinvent" was the word that those involved with the movie used.