I'm currently having this problem under the same circumstances as OP. An alien Sim in disguise. However, all of her outfits have the reverted eyebrow, not just her everyday.
Could you provide your save game ?
(see above)
I have that bug too. I kept going to all CAS mods, clothes, change sim, alter disguise, everything, and my sims eyebrows would still be pink instead of brown. I downloaded custom eyebrows, Maxis Match design, and it solved this issue for me. Still can't use in-game eyebrows, but I don't miss them. :P
