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I have had 5 yorkies, Poodles and mini Schnauzers, I never had one that would cry upon waking up. If Louie was neutered any baby teeth that had not come out on their own would have been removed when he was neutered. If he wasn't neutered he may have some baby teeth still remaining, they wold have to be removed by a vet.
In any case, I would have him checked out with your vet.
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