The harm is that the SWF shoots out the good intestinal flora along with all of the bad stuff you're shooting out (pun intended). It's really not appropriate or healthy to do the SWF when you aren't doing some kind of fasting or when your digestion is shut down through cleansing.
When you've completed your goal with the MC, be sure to repopulate your intestinal flora with probiotics. You can use yogurt or kefir or Probiotic suppliments from the healthfood store. You shouldn't really need any digestive aids other than that.