I change townies all the time in Sims Surgery but I'm a bit anal about the fact that their thumbnail still stays the same so what I usually do is make archetype Sims in CAS, that way I can decide their clothes as well as their other features. Then I make them into a family and keep them in the Sim bin. Exit out of the game and go into Sim Pe's Sim Surgery. I usually name the archetypes with the first name of the Sim they will replace so it's easier to find the two together and just replace them. The new face shows up in the thumbnail and when I go back into the game, I delete the family in the Sim Bin.
Another possibly easier way I discovered, if you just want to change their skintone is to do so in Sim Surgery and then go into the game and control the NPC you changed and take them to the mirror to change appearance. Their new skin tone will then show up in their thumbnail. Depending on how many townies you want to change, this can be convenient or a complete hassle. I only use it when there are a couple of townies who weren't too ugly for me to completely change but I wanted to make a few adjustments.