My son got better on the prednisone, but still experienced occasional stomach pain and symptoms. It just took many months for things to heal up and get to a place where he felt no pain, ate well, and the headaches and tiredness went away. He is in very solid remission now, so hang in there it can take a while.
If you feel like you are getting worse, definitely talk to your GI. Some people need a higher dose, need IV prednisone, slower taper, or prednisone just doesn't seem to affect their disease.
(((((Hugs)))))