Your little spiel means nothing i'm afraid and proves nothing in regards to assertion that the bile ducts can hold thousands of stones.
Simple fact is the stones are just bile that have had no option but to clump together in the intestines because the bile all shoots out in a relatively short space of time. A congealing process is bound to occur.
I guarantee your wife will release thousands more stones if she continues to flush regardless of her previous six. Eventually something will twig with liver and the process will start again. I got no stones for a long time and then start getting loads again. It's strange why the liver does go through sluggish spells but it happens nevertheless. Get her to do a night and morning flush and that will open the floodgates again.