Afraid your going to have to provide more info if you would like some advice.
You have inflammation for an unspecified reason and your being tested for something else (again you haven't said what) and you want to know someone to tell you how you will respond?
Treatment for what? Do you have pouchitis, cuffitis, arthritus, cancer, strictures, hernias, in grown toenails? All have different treatment options with different side effects
Why do you think treatment for a bowel condition would affect your knee?