My sim baby changed skin tone when growing from baby to toddler. I want to change just her skin tones, without cloning another sim full body. I don't want to change anything else. Insim, can only change a few things but not skin tone or eye color. I'm very happy with my sim facial structure, so cloning another toddler in SimPE to replace this on won't do at all.

If skin tone changed growing up, that probably just means there's something wrong with the skin.

Probably a borked skin.
Tutorial on how to fix it with SimPE: http://www.insimenator.org/index.php?topic=84275.0

Make sure to NOT delete the other sim if you made them with CAS just for this purpose (see XPTL's note). The best thing would be to find another sim in the neighborhood who already uses the skin you want your sim to use, or set the sim to use one of the default S1-S4 skins.

Another alternative is to figure out which skin the sim is using, and open it up in SimPE to see what the problem is. Could be missing texture files or other resources, or wrongly linked resources, or the baby skin isn't properly done but the rest is, or a skin made just for adult sims where the younger sims don't have properly made textures, or any of the sort.