I remember a few months ago, the forum had a study on a link between high altitudes and aggravation of flares in UCer's. So, I would say anything is possible, but to cushion your nerves, I've flown a few times now since being diagnosed and cannot say anything has changed much. =/
---EDIT
And what do you know! I look up news for colitis & crohns and find this
www.empowher.com/inflammatory-bowel-disease/content/whats-new-inflammatory-bowel-disease-research news piece mentioning high altitudes!