My GI doctor tried to scope me while I was flaring a few years back and only was able to go up 20 cm. All that crappy prep for naught! From then on, he wouldn't dare attempt a scope on me while I was in a flare. He said he was afraid of perferating the ulcers. Make sense to me.
I was hospitalized last May for UC and my fifth day I was scoped but the GI doctor used a pediatric scope on me. Very narrow.
So in answer to your question. NO...I wouldn't go through a colonoscopy while flaring. Explain to your doctor that you would rather wait till you are in remission. Furthermore...you just had a scope five months ago! My scope was last May and my doctor isn't pushing for me to have another one yet.