UPDATED PROBLEM SUMMARY:
Racemenu never cleans up obsolete overrides and overlays. Instead it assumes that mods using racemenu are responsible to clean up no longer needed textures. This bad design is made worse, by overrides and overlays propagating into racemenu presets. And then on top of this skyrim doesn't clean up itself either, unless you restart it, so it's very easy for invalid overrides and overlays spill over between savegames. Mechanically this is the same situation that
Fix is to be loaded after PNS, with PNS unaltered loaded before it. You can't really remove PNS anymore without potentially bricking your save, so the best we can do is disable it and turn the virus into a vaccine as it were.
As for what it removes:
The spell (ability) added to all npcs. This is what would most likely brick your save if PNS was removed.
The skin override added to all npcs. I am not familiar with skin overrides, but considering the function takes a key