I had something similar happen with the faces, the better looking ones with Seraphim body Mod were looking great until the Mod got an update, and for some reason they went back to the vanilla fugly faces - nothing I did corrected it... Then I deliberately forced the game to glitch by putting the Seraphim body Mod in the wrong place forcing the game to crash to the dashboard - then I put the Mod in the correct place again, and lo-and-behold, everything was working fine again.
Try that maybe?