I ran into this problem once. As a small part of a mod, I made a few changes that should have produced a significant visual difference, but it didn't appear to. When I encountered the NPC in game, the changes were there. When I checked back in the CS, the changes were there too. That's only happened to me once, though. Try making a few test NPCs with no AI, make changes to their appearances (and document them), place them in game and see if the changes show up.
Edit: I should have mentioned that the "changes" were done to a custom NPC.