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Well when he was a kid he just mistook her for Alice (as they shared the same body) but after the Tragedy when he and Gil fell into the "core of the Abyss" he met Alyss (still mistaking her for a white-haired Alice though). He eventually got spat out of the Abyss, and over time he could have put 2 and 2 together and understand that who he had met was the Will (Ta-DA my grand theory)however bear in mind its not really stated whether he truly remembered what had happened...ohohoho...but he most likely did (implied) ;)

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