I had some ugly twins that I wanted to change. I changed their faces when they were toddlers by making a pretty archetype sim and changing their faces on SimPE using the 'Plastic Surgery' option. It worked and I had no problem. However, I regretted their faces once they became teens cause they look very similar to a couple of sims from different families. I didn't want my sims to have a same face syndrome so I made an another archetype who looks different.

Now for the issue. I performed the standard plastic surgery and one twin got changed. The other one's face stayed the same. I tried it FIVE times, even once copying her twin sister's face and nothing has worked. Sometimes she wouldn't have makeup and brows on but still has her old face once I use the mirror and sometimes she would be completely unchanged as If did nothing on SimPe. I used 'Plastic Surgery' many times and I have no idea why I doesn't work sometimes.

Can you change her face in-game with the actual plastic surgery machine? That's not really a solution to your problem but it might be a workaround way to give her a different face or, at least, maybe it can help diagnose what the problem is.

I did and it didn't work. Oh well, I change the face to look as close to the other twin. Her original face is still pretty.

If you want to transfer the precise face from one person to another, you can copy the LXNR facial structure from one character file into another using SimPe. Then use a makeover dialog twice to refresh the model and portrait. The instance number for a basic person is 1. When you use the modify facial structure dialog (from within the game), a new facial structure is created with instance number 2, and used in most places. The original is still kept. It shows up in the buy clothes dialog, and maybe some other places. You can take the modified face and make it 1.

Make a backup of the character files in case something goes wrong.