If the sims are still ok, then you're good to go. But to test that you'll need to copy over your mods folder to the new game. It's easy to put a file somewhere other than the mods folder by accident. If they don't, then, you've probably missed something when you moved out your cc. If they do, then the save may be damaged and you'll have to decide whether you want to abandon it or continue playing as it is. If they don't, then copy over just your saves folder from your original 'The Sims 4' folder and start the game and look around to see if any of the NPCs you saw with the missing faces still have the problem. If they do, then I suggest a game repair.
Then after you get through the new sim, etc., take a look at the NPCs to see if they have any problems.
Just to be sure that it is the game rather than cc or mods, have you tried making a new vanilla game by letting the game create a new 'The Sims 4' folder? Just rename your current folder to something else.
