I am not entirely convinced that the existence of "stones" in the liver is disproved by this method.
You need control groups.
Will the dye be absorbed by an expelled stone? Many stones are porous, bricks are porous, coral is porous, even concrete. Quicklime added to mortar helps it to repel water in liquid form, but water vapor can still pass. Oil does penetrate stones.
So even though you have expelled colored stones, there is no possible conclusion that can be drawn until the absorption properties of the expelled stones can be revealed. Even then it may be different than the environment where it is immersed in bile... it may be in a gel like state in the liver. Is that enough to choke a liver?
My mother's gal bladder was removed because it was "fatty". Is there a biological response to the oil that causes stones to melt and then as they pass into digestive track and away from the biological response they then precipitate again? Or gel up and then dehydrate into precipitates in the large intestine? Too many unanswered possibilities.