I use Japanese waterstones in sharpening my handtools and here is a simple way to keep your stones flat. Lay a sheet of fine drywall screen on top of a thick sheet of glass, marble or other hard, flat surface, spritz your waterstone with water and scrub it on the screen. It doesn't take long to bring your waterstone back to a perfectly flat surface.
You can also use drywall screen to flatten the backs of old chisels and plane irons. By lapping the back and keeping firm pressure on top of the blade, toward the cutting edge, drywall screens will very quickly remove gunk and flatten a blade.
It took literally 20 seconds to achieve just this amount of polish and flattening.