Having assisted during sigmoidoscopy procedures (the sig does not reach up as "high" in the colon and the colonoscopy procedure), I will say this:

Patients follow a rigorous cleaning procedure prior to the scope insertion. I've not yet seen any patient who did not have lots of material to be "cleansed" prior to the procedure. It is not possible to scope someone whose bowel is not cleansed prior to the procedure because the scope simply becomes clogged if the fecal matter is not removed first.

That's why the inside of the bowel appears pink and healthy...because the material has all been removed first. Not to say that the bowel is unhealthy...just saying it does NOT normally appear as you see it on the screen during the exam.

Secondly I will say that there ARE places where fecal material "hides" within the bowel lining itself. This is a severe problem for folks with diverticulitis because the material gets caught and causes irritation, inflammation and (sometimes) infection. This is not the norm, however.

So, is a colon cleansing program going to be harmful? Probably not if done in a correct fashion. It is not usually necessary to replace the bacterial colonies of the colon as this will naturally occur following a scope procedure without any "help".