Crystal Creations jewelry wipes CAS jewelry if worn and then removed.

I don't believe this is a bug. Makeup is handled a bit differently, it uses what's called an Appearance Modifier. For the duration of the buff, the Sim has the appearance modifier active, and it overrides their standard appearance, but does not actually change their standard appearance.

Jewelry is being equipped same as if it was equipped in CAS. It's not being added via a buff that manages its existence. 

The game can make clothing change temporarily without overriding it, but that's for situational outfits and the like. When you;'re putting jewelry on you're not doing it for a temporary situation- it's either on or it's not, and it's on either one outfit or all outfits. 

I'm not sure there's a better way to handle it- you just need to mentally recontexualize it as "changing out what jewelry they're wearing". Having the game remember what they had on before, track it somewhere, and re-apply it when removed would be a lot more complicated than the way other appearance modifiers work, I think.