I am so sorry your Jax is having ear problems. I can tell you that YES, they can get middle ear infections. My late Molly had that happen, she also had a burst ear drum which can be very painful until it's healed.
I highly suggest you find another Vet who is well informed in the working of the ear. If that means going to a specialist I would do it. Ear infections that are on going and go the middle ear without healing can very possibly lead to hearing loss.
I pray your baby will be OK.
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