My sims in the game now are wearing non genetic pixie skins. I want to replace them with genetic pixie skins. The files they have same name. After I replace non-genetic with genetic of same file type - when I enter my game will my sims still be "wearing" their skins (not defaulting to townie)? Yes, I know to back up.

So long as both versions have the same skin tone in the Skin XML, then yes, your Sims will use the genetic versions. I'm guessing they will, so you should be fine.

If your Sims do revert to S2 skin, then it's pretty easy to give the skins you prefer genetic values with SimPE. I found this tutorial by Quinctia the easiest to follow.

Okay thank you but for me I want the children to inherit the skin so to change it after in SimPE would not be good I think. I have the game backed up in case this should fail.

Genetic values wouldn't change the skintone, just its value and thus making it available as an "in-between" skintone. But I think you should just try out the geneticized Pixie skins, see if your Sims still have their skintone, and like you said, keep back ups, because back ups are always handy. Most likely, they will have the same skintone value as the non-geneticized ones, and that's all that really matters in order to preserve your Sims' genetics.

To add info this is what the files look like. The Clean Installer will not show pink copy because it thinks of them as different so I will have to go thru and read carefully each one to replace. I worry, if Clean Installer does not think of them as same maybe also the game will not.

Since I don't really use Enayla's skins, I'm not sure where you got your geneticized version from. But here's what I found.

Enayla's Pixie Amethyst, non-geneticized, was geneticized, along with other skins, by Madame Mim at Genensims. I downloaded both those files and compared their Skintone XML in SimPE. They have the exact same skintone, so those would be safe to replace your original skins with.

I'm scarcely an expert at any of this, but Clean Installer may not show them as duplicates because the geneticized files have been altered and thus are now different files. Would you like to tell me who you are downloading these genetic versions from and I can check them in SimPE for you?

I got them from LiveJournal Link because she seemed to have the most of them and I want all the pixie skins. So far my born in game sims are still wearing the pixie skins that I replaced so I think it will work. Pic below of them after I replaced:
click pic to make large

Looks like you'll be fine. They'd have S2 skins if they hadn't recognized the Pixie skins.

I double-checked Enayla's file and the livejournal you linked to, and the geneticized versions are definitely the same as Enayla's. They have the exact same family number in the Skintone XML. So, your Sims and their babies to come should be a-ok.