The SWF is pretty benign in that it's more like a rinse than anything else since the way it works is that the recipe 2 tsp per 32 oz is the same specific gravity as blood so it passes through the system unabsorbed so it should not have caused any of the issues you are describing.
Are you doing it along with fasting? In any case it needs to be done 1st thing in the morning on an empty system. It is NOT a colon cleanser just a mild "rinse".
The SWF can deplete the intestinal flora but that is more with prolonged use and when doing it daily when fasting if you are just doing it every now and then you should look else where for your issues but in any case doing probiotics is always a good idea. My personal fave is Kefir. I drink it daily as regular routine