I came here from your werewolf mod on nexus. Is there any way you could make it to where your eye mod affects the player model when a mod or console command changes the player model to a werewolf? For watever reason that model has no eyes either.
Oh wow... I have no idea how the game handles something like changing the player character model to a non-humanoid ‘creature’ model. I suspect that, in your case, that because the game doesn’t expect the PC to be a werewolf, it’s still trying to use the eyemesh (and texture) from the (humanoid) morph stored in the save. (Eyes are a separate mesh from the rest of the head.)
You might want to try extracting the player character morph from a save (with DA Face Replacer), editing the MOR with pyGFF, to change the eye mesh to the one used by the NPC werewolves, and then reimporting the edited MOR into the save. (I like to use DAO Saves for that, but IIRC, you might be able to use the face replacer utility.)
Be sure to make a backup of your save in case something goes wrong, because that’s all a lot of wild speculation and guesswork on my part.
Good luck!