Feeding problems.

Hello parents! My son recently went to food therapy and they found out that my son is not doing good with his swallowing especially his age (12months) they’re thinking maybe it could be an acid reflux since he throws up when he eats or it could be something internal problem. We scheduled for a specialist for a swallow study and G.I specialist. I want to try different things like giving him only formula after lunch and after dinner. His doctors wants him in formula since he’s not eating 3x a day. But i was thinking maybe it could the milk that stopping him from eating? I noticed also that he is swallowing food without gagging and throwing up when he likes it. So i want to try different method. Give him milk after lunch and dinner . But his pedia said don’t do it cause we could starve him since he’s not eating regularly yet. How many times a day you give your 12month old milk? Is 2x a day be enough?