My opinion due to past experience is in answer to your questions:
1. I don't believe a colonoscopy will strip you of the good bacteria. My GI doctor always schedules one when I am out of flares and having colonoscopies NEVER brought about any of my flares, so hope that puts your mind at ease.
2. It is best to remove polyps, they are precancerous growths and should be removed. Your stool may have a bit of blood following a colonoscopy but I wouldn't worry about flaring from this.
3. Yes, a harmless polyp can morph into a malignancy if left there long enough. I have no idea how long this would take but I would want it OUT as soon as possible.
You're staying on top of things and I wouldn't worry.
62 yr old granny. South Jersey
Diagnosed with ulcerative proctitis in 1998 in hospital
Hospitalized (2nd time) in May 2008
Update 11/03/08...finally in remission!! Hope I don't jinx myself. Off the prednisone since 11/01/08...now see if I can stay off for longer than two weeks. Other meds: 6MP (75 mgm), colazal (6 per day), Benicar and Toprol (high blood pressure meds), Probiotic (2 per day), fish oil capsule and multi-vitamin and calcium with vitamin D.