If you are doing the hulda clark flush, it will not hurt the kidney.
I have always seen stones days after flushing. These are stones that were stuck in the liver and gradually break loose.
They are much smaller in size than gallstones because they can grow bigger bouncing around in the gallbladder, but they don't grow much in the liver.
As the mushroom shaped stones that initally plug the exit of the liver, flush out, the smaller stones inside start to gradually work closer toward the exit.