He knew the worms were down there and what they were capable of so why in travelers sake would he allow them to continue into the deep after they ignored his warnings. The sisters had no power then and he could have easily stopped them from unleashing the evil of the worms. Instead the sisters go on to become gods and the Leviathan gets eaten.
Been studing the lore alot more as of recently and this kinda bugs me. Maybe i missed something
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My thoughts being a huge fan of lore, the leviathan couldn't touch them as they weren't from the same plane yet.. Once the sisters became ascendant they were able to enter the plane of the leviathan.. And destroy him.. Turning that plane into their "Throne" world.. The only plane in which they themselves can be destroyed.