I will second what mike has said. This is really good but it is hard to say exactly how it effects the flora in the body as they might never reach it.
About 90% of digestion and absorption occurs in the (healthy) small intestines. However I could see this number drastically changing for those that are having trouble producing bile or have mucoid plaque lining their small intestines. These factors could then allow these things to flow into the large intestines and wreak havoc on the good bacteria.
With that being said maybe it would be better to follow a "killing" protocol after a colon flush (PB shakes) and liver/gallbladder flush. Also it is always a good idea to try and add some good flora to the mix afterward.