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If I'm understanding correctly, you have a previous save where one or more of your sims was using a cc skin and you no longer have that skin in game? If so it's not a real big deal. The skin will be replaced by an EA one on the sim(s) affected. They might look weird initially ( that also happens when you dl a sim , but not the cc skin that was intended for them). That's easy to fix though, just take them to CAS and select a different skin, hair or anything even temporarily and their look will then be okay again.You can continue using the EA skin or give them a different cc one, either way. If you track down the cc skin later, just send them to CAS and slap it on them. No other aspects of the game should be affected by any of that.
If the sim was wearing a non-default replacement skin, they will end up black. Again, not a game-breaker. Just take them into CAS and give them another one.
Or you can leave them that way. It doesn't hurt anything.