If you want a gradual fade over distance, you can use the altitude terrain shader in the alpha channel. It can be set to work in the X, Y or Z axis (which is a little odd because the name implies it only works in the Z axis), over Global or Local space and can be animated for the height value. Fiddle with the blend value in the shader and the tweeners in the timeline to get a nice transition.
You could use it from as a reference shader in the alpha channel if you need each stone to have a unique colour shader.
I was hoping to be able to get ‘procedural lock’ to work with it so that any angle could be used but, unfortunately, that doesn’t seem to be possible.
That shouldn’t be a huge problem if you’re ok with the effect working along a primary axis.
If you’re just wanting sudden dissapearances of selected stones, then I’d suggest creating multiple groups and switching the visibility off on the groups as needed.