I was in the exact boat a year ago with my son. Potty was going well but he would not go poop unless in a pullup. I tried the method of having him move into the bathroom to poop in a pullup, then on the toilet. No luck. This went on for 6 months!
What worked for us was Miralax, recommended by the doctor. While my son was not constipated, his poop was firm enough to "freak" him out, I guess. As soon as we softened his poop, he easily started pooping in the toilet. It took about a week on Miralax to get it to the right consistency for him (I know, too much info) After that we found a half dose daily was the key.
Talk to your doctor before you but her on it though. I hope this helps you. I wish someone had given me this advice much sooner!