It's highly unlikely that doing 3 SWF killed your intestinal flora. The SWF is not a fix for constipation it is more or less a "rinse" for the GI tract. You should look into colon cleanses and what you are eating for your solution.
Kefir is a much better probiotic than yogurt as yogurt only contain one type of probiotic bacteria which is transient. Kefir on the other hand contains something like 10 or 12 different bacterial strains that can actually colonize in your gut.