(Spoilers) So when Axel comes back from CO...

[Chrono Mizaki]

Originally Posted by Mr. Wilhelm

See it like Star Wars. The novels are canon, they are the expanded universe, but once the game contradicts the novels, the contradicted part of the novel becomes non canon, exactly like when a SW movie contradicts the expanded universe, this part of the EU becomes non canon.

And this is why you should never trust Square-Enix with continuity, especially the likes of Chrono Cross and Advent Children ;D They are bound to fuck something up. I admit they improved tremendously, but they still have flaws with details in continuity.