Storyline between classes?

It was. However:

Doesn't make sense really. We know for a fact that the seal stone was in trus possesion in the present. Even if they were the same, he got his hands on it in the immediate timeline, regardless of how the past went, whether they were the same and someone else stole it back, or they're different stones, its now safe, unless the black wings at some point steal it again from rien.

Edit: of course, that doesn't mean the black wings couldn't have already gone and done whatever they needed the stone for in the time between them taking it from ellin, and tru finding it again. We don't really have enough specific details to say they need them all at once for reviving the black mage, just that they needed them for ...something. Without more information, we can't really tell. Unless that comes up in the resistance storyline somewhere, we don't really know