I'm sorry to hear this
Before my first big flare and diagnosis a few years ago I was over a year deep into endurance training, specifically running with strength training using plyometrics and weightlifting throughout the week as well. I ended up having to stop everything because I was so fatigued. I needed to recover, regain weight that started to come off (I cannot afford to lose) and stop the bleeding. I moved to yoga and pilates as my exercise when I could. After a few months I was doing much better, the meds kicked in and I again started to endurance train, climb my mountains and go on extended hikes. Within a few months I became totally symptomatic and had to repeat, here is where pred started being used. I have had this vicious cycle repeat every 4-6 months or so since. I also had a heavy endurance industry job which I am most likely going to have to give up. I never noticed a correlation between my endurance training causing my inflammation or not but the timing is interesting when I look back now that you mention it.
I will probably start a new med when I see my GI doc in a week and a half at his suggestion which I initially balked at - after a lot of thought and discussion and reading on the forum here, I am hoping more than anything that something like Remicade will give me my life and my physical endurance back. I am willing to get a new job but having a healthy physically active lifestyle is so important to me too.
I look forward to hearing anyone else's experience with this. I need to say: whatever happens don't give up, do what you can do only when you can do it, and don't be too hard on yourself. The last one I am still working on myself.