Dear Ann,
Yes, this will improve over time as your son continues to use the potty and experience no discomfort. Be sure to keep up your efforts around his diet so that his stools do not become hard and promote discomfort - this would only increase his reticence.
My daughter who is 4 now went through this same thing about 4 or 5 months ago. She would hold in her BM's for days.. I made sure she had lots of foods that helped to keep her stools loose. She still would try to hold them in. I ended up taking her to the doctor to make sure nothing was wrong, and he suggested for me to give her an enema. I know it sounds extreme, but she had gone 5 days without a movement, and was surely backed up. Well, the enema worked, it was quite an experience for my daughter, but now she goes on her own, and back then all I had to let her know is that we would have to do another enema if she chose not to go potty, and let me tell you, it didnt take her long to figure out that going "poopie" was way better than having one of those enemas. I also would praise her to high heaven when she did pass her bowels.. and we would say "bye-bye" to them as they got flushed down. Another thing that helped is I would tell her that she needed to make room in her tummy for more food, and that she had to let the old food come out. Sounds silly, but works. Goodluck! Christine