That seems to be a common thing that happens to people. The symptoms get worse as the old stones move forward in the liver. For me, my Depression got worse, I was an emotional wreck for some weeks when I began flushing. I continued to flush and now I'm more emotionally stable than I've ever been in my life. I'm still working on other health issues though, mainly my skin.
So yeah, keep going! But also make sure your bowels are working as they should be. Drink lots of water, and eat a vegan diet high in fiber. You could also do enemas if you want to.