Lip color data seems to be lost whenever saving an NPC in the Creation Kit. If you need to change an NPC's face tinting and you don't want to lose lip color:

• First make the edits you want.
  
• Now generate the face tint data by highlighting the NPC you changed in the object window and pressing Ctrl+F4. Feel free to discard the TGA file. You only need the DDS.
  
• Open up Skyrim - Textures.BSA. I use FOMM to do this.
  
• Unpack the face tint data for the NPC you changed.
  
• Open both versions of the face tint - the one you unpacked and the original. I use the GIMP with DDS plugin for this.
  
• Manually edit your version to include the lip color from the original. Feel free to make any color changes now. Mind the background - it's not just for show. That's the skin tint.
  
• Choose Save As when saving this file. In the GIMP, you must choose Save As to get the option appearing to generate mipmaps.

Hope this helps anyone who wanted to change NPC face tint. Here's an example where I've changed Illia's face structure, hair style, eyebrows, and face tinting.
http://static.skyrim.nexusmods.com/downloads/images/7245-1-1328722614.jpg

http://skyrim.nexusmods.com/downloads/file.php?id=1920 was used in this screenshot.

This is useful for people to know, so I'll give it a bump.

Did you have trouble previewing Illia in the preview window? Nothing shows up when I check face preview and I get an error when checking full preview (the exclamation mark appears). I also see the exclamation mark in the render window. Wondering if it's an error on my end.

No, I don't quite have that problem. I do know that the pale lips thing has been mentioned elsewhere though, so that issue isn't mine alone.