This is an anxiety issue J., not a training issue. Your son is upset that his poop will be flushed down the toilet, and he may even be worried that he will fall into it and be flushed down himself. When he poops in his diaper, he feels safe.
Start by flushing the poop from his diaper when he is NOT AROUND, or when he may not be aware that it is happening. It is when parents are in a hurry to flush poop, and do it in front of kids, that kids with anxiety begin to resist potty training.
Gently find out where his "safe" place is to poop (where he disappears to) and put the potty chair there for him. It is probably a long way from the bathroom. Don't be attached to him using it at first, just put it there and wait for him to feel safe taking off his diaper himself.
I believe that little boys may be considered harder to train because they are more sensitive than girls, and most parents believe that they shouldn't be sensitive for some reason. In actuality, boys are not as analytical as girls and tend to think in black and white: "My poop is part of me, she has flushed it down the toilet, she has flushed ME down the toilet..."
Read him the books: Everybody Poops. Once Upon a Potty. Read, read, read to him children's stories about pooping and about ANXIETY (check out the Francis books). Then talk to him about what his fears are so that he knows that you care about his feelings.
Mirroring his feelings back to him will help: "Wow, it sounds like you are really worried about...."
Boys are amazingly sensitive and need more help sorting out their feelings. Doing this now will help him to become a sensitive man down the road. Neglecting it will ensure that he is just like the rest of them.