@dval – What a terrible experience having a flare up happen overnight! It seems to me that you are one of very few with IBD that got a flare up right after the flushot. I'm aware that there is no proof found yet that there is a connection, but there are several reports describing a reaction that you had – happening out of the blue right after the flushot. It is also so important for you and others with IBD to get the flushot.
Your Gastroenterologist sounds great, having a plan for you immediately. If Entyvio has worked so well for you, but you hesitate to get more frequent infusions you could ask your doctor to go over risks and side effects again.
You are wise to see that you have to be your own health advocate. That is what I have done for years. I don't have UC or Crohns, but other autoimmune GI disease. I have seen connections in my illness but doctors claim there is no evidence. Many times, the evidence will come after a few years!
We would appreciate it very much if you can get back to us when you know more.