Hmm....Vanitas said this in the additional cutscene in Re:Mind:
I know you're talking about the time in BBS, but I don't really understand why Vanitas would say this if it didn't happen before, because since this Vanitas is from the future, his heart will return back to the past upon being defeated, so what he's saying here wouldn't exactly apply to his present form. I don't know, it seems pretty clear to me that Vanitas returned to Ventus's heart.
Isn't that impossible? The arks in Daybreak Town were incomplete, and only the incomplete ones can transcend time. The one in Radiant Garden is a complete one, as it transported Kairi across space, not time.