I went into Simpe to check and she has the custom eye color listed for her DNA.
I figured that since you knew how to check the DNA code that you would know how to copy the code (ctrl+c) and paste it (ctrl+v) into the eye line in the sims "character file" under "age data"
after doing that you just commit and save and then go in-game and have the sim change appearence in a mirror.
Okay, so I did do it right. I have done this once before on two other sims and it worked fine but on this particular sim (and her son), it doesn't work. I have no idea why, so I figured I must be doing something wrong.