dokiyuri

The SetNpcWeight command seemed to change Lydia's eyes right, although you have to figure out the npc that you're dealing with's weight. (Lydia is 100 by default) And to be noted, if you have mods enabled, she will then change her textures and whatnot to those you have currently installed. So if you like how she looks in the vanilla game, you have to uninstall a lot of appearance mods.