Firstly I would say the Clarkia did work. The section on Allergies in The Cure For All Diseases goes into some detail on liver flukes. They have two suckers with which to hold onto their host very tight. They only lose their grip when they die. I would assume it was the Clarkia that killed them.
As long as you do follow-up ("maintenance") for parasite cleansing your liver shouldn't be troubled with more live parasites. And you are managing to get the dead ones out. You may find that with the next Liver Flush you get more stones out.
I did the same as you, Clarkia followed by liver flush. I saw no flukes but about 2,500 black threads which may have been strings of eggs and may have come from the ovaries of flukes in my liver. It may be that the Clarkia killed the parents, whose ovaries then burst and discharged strings of eggs, but the parents didn't come out, only the strings of eggs.
Unfortunately it's not conclusive that my black threads were really strings of eggs because I never saw, or at least never noticed, any parent. You're more fortunate than me because at least you can be sure of the results of your parasite cleanse.