I'm not sure if this is dealt in any of the other threads, but after Terra Tower assumes its original Dinopolis shape, Belthasar leaves Viper Manor. The room to the Neo Epoch simply "won't open."
This could be one of the very few launching points of our shaping the world after Chrono Cross. Where do you think Belthasar went? My money's on the future. I realize this will be mostly pure speculation, but it's necessary. I also believe he may have left simply to avoid being caught up in the dimensional unification, if indeed it did run a sort of "median filter" on both dimensions. That could have proved troublesome if Belthasar's own history was rewritten.