The native bacteria isn't really in the liver -- it's mostly in the intestinal tract, though our entire body is really a colony of organisms. And I've not heard that cleaning the colon disrupts beneficial bacteria, though it's certainly possible to do that in theory, I suppose, if you did it all the time. Periodic cleansing, either by fasting or cleansing, would seem to present a more hospitable environment for beneficial organisms by keeping it healthy, but who knows?