In this case director resigned for health reasons (whatever it means) and intially Yokohama Animation Lab were only producing the anime, while the actual animation was handled by Cloud Hearts. Tру studios are probably related considering how much they collaborate. But in this case the change was probably forced later by production commitee.
Either director got sick because production was behind the schedule and they got themselves owerworked or directors health issues affected the production but it took some time for them to react.
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