Bacillus Subtilis is a very beneficial bacteria and improves absorption of nutrients by increasing the size of the intestinal villi and it naturally passes out of the digestive system and does not implant. It is not directly responsible for your problems. Your more likely reacting to the other things that you are taking! Stop those first and things should slowly improve. Diarrhoea will weaken you if it goes on for long.
Enemas are not bad, where did you get that idea from? They do not affect the bacteria of the bowel, much of which is protected by a biofilm, yes there are beneficial biofilms too or they are implanted so they will not be flushed by a little bit of water. A colonic does not dislodge them so an enema certainly won't. An enema will flush out the mass of waste which usually passes through the colon. It's only if there are implant locations that any of those can take up residence. The bowel flora rarely change, if you started with unhelpful bacteria, from your mother, then you will continue most of your life with largely the same ones.