I was scoped in June after a year of constant antibiotics with two weeks off prior to the scope and inflammation was also found (according to GI --all people with pouches has some inflammation in them). He suggested I need NOT go back on antibiotics and I have half-heartedly followed his advice as my symptoms return also when off them. I oscillate between missing a few days and then taking some intermittently when the symptoms get worse (prob not a great way of managing it). I also struggle with chronic cuffitis/hence butt burn which is very annoying.
My biggest pouchitis complaint is ALWAYS feeling like I have been hit by a truck in that every joint and muscle in my body aches and it is like having the flu 24/7. In your case if you are having increased and bothersome symptoms it does make sense to stay on the antibiotics longer and I would think that you may want to postpone anything that would put more stress on your body when you are recovering and trying to feel better.
I am seeing my GI to talk about possible other medication options like enocort today for my pouchitis because after a solid year of dealing with this, I am ready to either yank the pouch or try some stronger treatment options.