Doing a lot of enemas and the same goes for taking a lot of laxatives will deplete your bowels of all bacteria, good and bad. This is why it is important to replenish the supply of enzymes both orally and rectally.
There are very few cases where someone died because of taking too many enemas. The one I remember was a woman who took over 10 deep enemas one after the other all in a period of one day. Her electrolytes got unbalanced and she died.
Too many of anything is bad for you. Too many vitamins, too many alcoholic drinks, too much fat, too much everything is bad for you. Taking a daily series enema for one or two weeks is okay. Some people have taken daily enemas for most of their lives with no ill effect. Most of them claim the contrary. So unless you are taking lots and lots of enemas don’t worry. You will lose some mucus coating of your bowels this is inevitable, the same happens with some of the harsh laxatives. Just make sure that after finishing a few days of enemas to take acidophilus replenishing enemas.
Please read my blog titled: “My challenge”; link below.
I hope this answers your questions.