I had the same problem on one Sim. What fixed it for me was going into full edit mode and altering the hair colors there. Didn't have a problem after that. Perhaps changing haircolors via "change appearance" doesn't make it permanent.
To go into full edit mode (basically taking you back to CAS but giving you full edit capabilities):
- Open the console (press Control+Shift+C)
- Type "testingcheats on" and press Enter (some people have to type "testingcheats true"). DO leave the space, but don't type the quotation marks.
- You should see a message saying cheats are now enabled (if not, try the "true" version)
- Type "cas.fulleditmode" (again, no quotation marks) and press Enter
- Shift-Click on the affected Sim and select the following option: Modify in CAS.
This should take you to the version of CAS where you can edit/change
everything: physical, Aspirations, traits, cosmetics, whatever.
When you're done and back in your game, some say it's adviseable to manually turn testingcheats off (although others say testingcheats automatically turns off the next time you encounter a loading screen). I don't know for sure which works -- I turn them off manually now, just to be on the safe side.
Hope that helps! Good luck :).
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Edited to reflect that it is definitely a
Shift-Click on the Sim and to specify the option's name "Modify in CAS"