You're talking about a gastro doc and not a general practitioner, right? I'm surprised he hasn't taken measures to increase his meds. He's already on prednisone? What type of stool and blood tests is he running? When do you see the doctor again?
For a flare that's bad enough for liquid diarrhea and blood, it's not going to resolve by itself.
There is no typical way for a flare to start... some come on suddenly with some sort of trigger, some come on gradually. Neither is there a typical length of time to flare. Depends on the severity of the symptoms and what your son's personal triggers might be. I wouldn't think physical activity would be to blame. Usually it's more about stress, a course of antibiotics, too much rich/sweet holiday food, etc.
Diagnosed with ulcerative colitis spring 1999.
Maintenance dose sulfasalazine.
Probiotics, l-glutamine and fish oil caps. George's aloe vera juice. Oregano oil antibiotic, antiviral, antifungal. Long-term remission with only minor blips.