Hi!
There is a fair bit of bio medium in the substrate, but if your filter is adequately sized and cycled it shouldn't be a problem. One of the main advantages of sand is that you do not have to remove it and clean it like you would gravel. It does not have gaps in the substrate that poop can fall into or algae can grow on, all it requires is a good vacuuming with a siphon, gravel vacuum or turkey buster once in a while when the poop builds up on the surface. If the actual sand has changed colour that is normal and doesn't necessarily meant its dirty. Some of the components of the sand turn darker with time and the substances in the water, and a lot of it is actually good bacteria. It might require a little bit of a move around to avoid gas build up but apart from the occasional maintenance you should be fine without removing it, so you can just leave the axolotl in the tank while this is happening. It would be much less stressful for him/her.
good luck