Interesting observation, one that I am sure everyone but me already knew. I had a working game, with my modified Eola as my companion. For some reason, I got the crazy idea to test out Apachiisky's optional colors. Rather than use my test game (involves some folder re-naming) I decided that it would be safe to use another modded NPC. So I used a copy of Lydia that I had saved out, dropped that .esp file in my (active) game, and started up with a coc to the castle, then setstage mq104 160 (end of dragon rising, where you get Lydia as housecarl). Saw what effect the mod had, decided that it was of no practical value, but I might use it in future. removed the mod, as well as Lydia's .esp file.

Later went into the game for a wee bit of dungeon diving. Did a few dungeons, then Eola and I went back to Breezehome. Naturally, Lydia (unmodified) was there, and to my surprise had grey-face syndrome.

Now, I had never made a savegame while Lydia's .esp was in the game, and there was not even an autosave made. I checked. So how did a vanilla NPC get grey-faced?