After 10 surgeries (mostly endoscopies) we discovered that Danny has an extremely rare disorder. It is called Isolated Chymotrypsin Deficiency. Basically your pancreas produces the enzymes that digest your food and he didn't make one of them. The four major ones work together so without that one he couldn't properly digest fats or proteins. We have reintroduced milk and he seems to do fine. It has been a six month process though mostly because he has been really sick lately. One illness after another.

He is one of 9 people in the world with his deficiency but it is the reason he had so many protein intolerances. Since he couldn't properly break down the protein his body recognized it as poison.
The only way to know out if they will outgrow the allergy/intolerance is to wait and see. There is no way to know if it will get worse, stay the same, or go away. Danny's allergist has us wait 1 year after a failed attempt to retry. We also have to wait one month between stages. A stage was like moving from really hard cheeses, like cheddar, to soft cheeses, like mozzarella. There were several other stages too which is why it took so long but we already had 3 failed attempts...all before he started the enzyme replacements. Protein intolerances can be tested but aren't very accurate until at least after 1 but still aren't very accurate until around the age of three. Blood tests are worse. They are somewhat guesses as to the severity or presence of an allergy and do not measure intolerances. Skin patch testing is best for protein intolerances but it is best not to test that way until she is at least a year old but longer if you can avoid it.
Having to avoid a food because of a protein intolerance can lead to an allergy due to that protein no longer being recognized by the body. It is then immediately seen as a poison and elicits an immune response....aka allergic reaction. If the protein is kept in the diet it is less likely they will develop an allergy to that food but the damage to the body can be worse than simply having an allergy....no matter how severe. Danny didn't develop any allergies after starting in Neocate Jr. He thrived on it for a few weeks then flat-lined again in weight. We found later that this was due to the enzyme deficiency. We slammed him with calories which sustained him at 21 pounds rather than 19.
I probably rambled a LOT but I hope I at least answered your questions.