Currently, sharestone positions and colors seem to be retained after removal. An example of this is having a colorless sharestone and breaking, coloring it, and replacing it in the same place, it will still be accessible from colorless sharestones. If you then move the colored sharestone, then the colorless sharestones don't seem to remove it and it just says the sharestone is being moved when you try to warp to it.

Minecraft version: 1.16.5
Forge version: 36.1.0
Waystones version: 7.6.2

Confirming this, the colorless ones also keep the previous names of the colored ones in the list.

Modpack: Valhesia 3.4.1
Minecraft: 1.16.5
Forge: 36.2.0

I tried to recolour an existing coloured sharestone after I silk touch mined it up, theorizing that it would keep the name after crafting, but the name data got removed from the item and is now stuck in the list with no source anymore. Don't know how to remove it from the list in survival mode.

It appears to me that when applying a colour to a sharestone, its current name is either not properly deleted from the list, or should be copied over to the newly crafted item.