Can confirm that on PC this still happens. No mods, no cheats, new save file. Had several caster babies from both caster parents. Toddler has special caster eyes when aged up from a baby. They are also half-alien, so I'm not sure if that matters. They have purple or blue skin, but still have hair and no disguise. The caster eyes look fine in CAS, but if their outfits are modified, the caster eyes are gone in live mode. I tried the suggestion here of changing just one clothing item, toggling to a different outfit, seeing their eyes still there, then exiting on the same sim. Their eyes were still changed to a standard color when switching back to live mode. I also confirmed this happens when changing outfits for children. The only way to get around this and keep their eyes (without mods) is to age them up to teenagers and then change the outfits. Teenagers and adults will keep the caster eyes. I think it's because toddlers and children are not officially casters until they age up. This causes the game to remove any caster features when they are edited in CAS.
Some more information. Even if you wait until they are a teenager, they can never change between caster eyes or ears. You're stuck with the ones you had at birth. If you ever change the eyes to a different color, then you can never get the original eyes back because the options aren't there. The only way to fix this is to go to the magic realm and ask for the rite of dissolution. This removes the spell caster occult from the sim and they're human again. Wait 1 sim day because of in game restrictions. Go back to the magic realm and ask to become a spell caster again. This time, all of the spell caster eyes and ears will be unlocked and you can have any of them. This also gets rid of the false 2nd form you might see when saving a spell caster by birth in CAS. You keep your inherited bloodline trait and any previous spells and caster rank you earned, so there is no penalty for resetting your caster like this. You just lose 1 day of in-game time while you're not a caster.
