Remember that the stones are formed in the liver, not the gallbladder. The stones simply flow into the gallbladder which is basically a sac for holding concentrated bile. (that is one reason doctors are so willing to cut it out) Of course as the gallbladder becomes more filled with stones, it releases less bile and more and more stones keep packing it tighter. This backup of stones in the gallbladder leads to even more liver congestion since even the bile backs up and stagnates in the liver. My advice is to keep on flushing for quite a while longer. It took me almost a year to have a stone free flush. I have passed well over 6000 stones of all sizes and colors. I still pass some stones although I am now just flushing every 4-6 weeks.
I am another strong advocate of the Hulda Clark flush, although I now follow the protocol of Andreas Moritz who suggests days of preflush preparation using apple juice, apple cider vinegar or malic acid tablets. It may be time to change your flushing procedure, at least temporarily, and go with the slightly more vigorous Clark flush.