I haven't tried to put my default replacement skins in, but all custom skintones may require updating, due to the fact that a sim's skin will now change tone if they are near freezing or overheated.
The toning is an effect similar to that seen on vampires, so it works on custom skintones just fine.
My default replacements for skins (Lin's v. of SimCribbling skins), eyes, and brows also work without a problem.