Does enema flush out the good bacteria from the intestines?
No, there is no such thing as enema flushing out the good bacteria in the intestines. You are only using 300-500 ml of water in your enema pot.
When the intestines are layered with toxic filth, old faeces and plaque, they cannot possibly create any good bacteria. Taking an enema clears the intestines of this waste so that they become healthy and clean again. Good bacteria can only thrive in clean intestines, not in dirty intestines.