Can severe choking cause brain atrophy in an infant?

Son has very delayed milestones.  Sat up first the first time at 11 months.  Walked by 16 months, but still wobbly 4 months later.  Has hypotonia, dyshagia (trouble eating, will sometimes refuse to swallow own saliva), abnormal eye movements, reflux, GERD, chronic constipation, babbles but doesn't speak.
Had an MRI that showed some brain atrophy in the temple area on both sides.  Etiology not known.  He had a severe choking incident at under 24 hrs of age.  He is so allergic to milk protein, he vomited up breast milk, started flailing, and stopped breathing.  The nurse couldn't get his airway clear, and ran off with him to the nursery.  He was choking for at least 1 minute, before the nurse ran off with him.  He made no sound, and turned blue.

One neurosurgeon, when asked what caused it, shrugged and said "birth?"  Another doctor said it was benign extra axial fluid of infancy.  When I asked him why, if it was benign, my son had all these things wrong with him, he responded:  "It's benign for most kids."  and walked out.

There were no problems at birth that I noticed (he is my 4th child-scheduled c-section), and seemed completely normal up until the choking incident.  The only thing that stands out in my mind is the choking incident.  He had about 6 more, but they weren't as long as the first.  I would say about 30 seconds to 1 minute long.  Elemental (feeding tube) formula, which is devoid of all milk protein, has stopped the choking incidents.  It took me 2 weeks to get him to a pediatric GI doctor.  My pediatrician kept telling me that "babies spit up."  I demanded a referral to the specialist.  I got it, and got yelled at in the process.  My son had a choking incident on the specialist's table.

Obviously, I'm very frustrated, not getting a straight answer.  Can a severe choking incident cause brain atrophy??  Would this be cerebral palsy??

I appreciate all responses:)