Reading about your baby and his illness makes me very sad and I can't even begin to imagine how you are feeling. Sounds like the meds to help him sleeping is causing the nighttime reactions but like others have suggested, please speak with his vet and if possible seek a second opinion. If only these babies could tell us in words what they are feeling we'd be so much better positioned to help but all we can rely on are tests/results and advice from vets and other pet parents.
I am praying for your baby and you.
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Romeo  and Sujata 
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