I delete all the cache files, it's the first thing I try.
Unfortunately there's no real pattern to how it happens other than it seems to be related to mermaids in particular for me. I haven't tested it with other sims yet. I got a bit discouraged because of how random it is. I haven't played in a month because of it, but I can probably go in and try to recreate what I'm seeing. Maybe something has been fixed since then, but this is what I'm doing at the time.
My process is:
I start a new CAS sim. I picked a mermaid. Settled on her face and body structure. Then picked a mermaid eye for her mermaid form and a human eye for her human form. I fight with eyes for the entire process of fixing up her outfits and finally get everything the way I want it. I enter her into a neighborhood to play and when I get in there, her eye color(both the occult and human) have defaulted to the basic black/brown eye color. Instead of exiting the neighborhood to get to CAS, I use the commands to get back into CAS where I make the changes again. I have a 50/50 shot for it to stick.