I don't really see this, as Elidibus's balance he spoke of turned out to really be his own role as mediator for the convocation bleeding into everything he did, as he lost more and more of himself that core principle became something he clung ever tightly, Zodiark himself hasn't really done anything since the sundering, which is kind of the point, he's often blamed for a lot of things he's had no direct or even indirect part in, we've yet to even ascertain his motivations, if he even has any. The final days 2.0 are no more his doing than the first ones were, Danny boy and Zenos are kicking these ones off, and while his heart is "dead"/trapped, he's been separated from it and effectively in a coma for 12000 years, so pretty much nothing has changed for him.
I don't see them going out of their way to of all things need Zodiark to suddenly need his heart back, they'll likely either have them fuse, they'll both stick around, or both need to go or one of them might remain, though given parts of Zodiark are still technically sealed in the other shards, I'm not even sure if he can be destroyed in the traditional sense.