The Black Chronicle can only be hurt if a Shadow is on the same tile as it. Gafka's Wind God Strike is perfect here since it forces every enemy onto the center tile. For the Apocrypha you should first try building up combos (Gafka's Musou and Aht's Dancing Death are perfect for that) so that the magic spells you should use do more damage. The only real annoying part is the Apocrypha's second stage since it likes to spam status ailments. Having Sky Drops equipped really helps here. Turn Breaks also helped tremendously.