This really does not disprove anything....

The fact that your Gallstones were black does not disprove the flush. In fact it kind of reinforces it.

I don't think I have ever heard of anyone passing black stones early in their flushing careers. Black stones DO come out though towards the end of your cleansings. It just makes sense that this is because they are not.. "fresh" stones. They've been in there a while. Which is also why they'd be seemingly impossibly hard to get out without surgery, but not impossible.