Everything that comes out in your BM from doing Liver-Flush is bad for your body otherwise body will hold on to it. Liver-Flush every two to three weeks apart is a good suggestion, till you stop getting the gallstones. Every living thing makes Gallstones in various degrees, some make more, some less.
I can tell you my body makes a lot of stones despite of my good diet. It has improved a bit over the years. Now in my flushes I see small light green stones.
When you eat junk foods, sugary foods, caffeine, high fat cholesterol ridden foods, then you make more stones. Lastly, your emotions also have a lot to do with forming of GB stones.
No one know how quickly one makes new stones. The answer to your question about Liver-Flush process killing the microbium in your gut, is no. I do not see any anti bacterial substances in olive oil, grapefruit juice and magnesium sulphate/citrate.
Do another flush.
How do you really feel after you first flush?
I think this whole thread belongs on Liver Flush Forum .