I'd probably just run dresser cleanup on one sim with missing things in their outfits first, to see if it fixes it. If it does, then I'd tell MCCC to run it on everyone.
To run it on one sim, click them and then choose "MC Command Center"->"MC Dresser"->"Outfit Commands"->"Clean Outfits". I have no idea if it will correct issues related to removed CC or not; I'm just curious if it will. NRAAS Dresser for TS3 did, and it was the inspiration for MCCC.
I use cleaner pretty regularly on my played Sims when they end up with outfits in situations where they are supposed to be nude (like showering). It is safe to use.