I see your message has been here for a while. No one has answered; so I'll try. You would have gotten a response on the Humaworm or parasiteSupport Forums .
Humaworm has said that the cleanse does kill the good with the bad. The herbs don't care whether they are friendly or not. I personally think that is a good thing. If both good and bad are being killed, the body is still in balance. You don't want too much of either one, no matter how symbiotic the relationship.
One reason you want friendly bacteria, is so that they will take all available seats in the colon, leaving none for the others. If you are on a parasite cleanse, the good bacteria will not be needed during that time.
BTW: good luck with building your family. It sounds like you are off to a healthy start.