J.,
A friend of mine has throat issues. Her esophagus is VERY small. She has always had to take very small bites, chew forever, and just in general be careful how she eats. A few years ago it was getting quite bad and she eventually saw a specialist. This condition has some very drastic procedures for severe cases. Thankfully the doctor determined her case was not severe and directed her to drink something WARM with all her meals. Once she started that, she hasn't had any further issues eating.
The warm liquid helps the muscle relax and allows the esophagus to expand as it is designed to do. Something cold to drink will make the muscle contract.
I would try to determine if it is a manipulation thing or if something is actually physically going on. If it is something physical, I would take him to see the doc. Keep in mind....when he gets hungry enough he will ask for food. Also, toddlers can have a real erratic diet. One day they are starving, the next they aren't hungry at all.
Good luck!