With previous Bethesda modding tools, you could convert an esp to an esm. Assuming that the plugin is called plugin.esp, the steps are:

• Rename plugin.esp to plugin.esm.
  
• Open plugin.esm in CK/GECK as an active file.
  
• Make an edit to some content in plugin and undo it.
  
• Save the plugin.

Step 4 will set the esm flag. Note that you could not continue to edit the esm after saving. I have no idea if this will work with the Skyrim CK.

What exactly did you mean with control F4 ? some sort of hotkey?

I've found a (slightly ugly) workaround for this:

• make a plugin containing only your NPC records
  
• convert it to a .esm using tesvsnip
  
• load it into the CK and follow the procedure JoelBurgess posted above to create the .dds and .tga files
  
• make the rest of your mod as a .esp file with the .esm you just created as an additional master

Using this method the NPC's face showed up perfectly with the proper skin tone, eye makeup, lipstick, etc.

EDIT: Damn! Ninja'd!

What JoelBurgess said.

PS: Do the new facegen dds files, after hitting cntrl f4 get packaged if you upload to steam for example?

Darkon, out of curiosity, is there any significant difference between the extra steps in your method versus Joel's method? It seems the only difference would be your method allows you to toggle off the changes, correct me if I'm wrong.

Brief EDIT: Joel's method (much thanks for this by the way) works like a charm. I created an ESP of the changes (after exporting the .dds and .tga files), and toggling it OFF caused the same peach colored mismatched skin tone - keeping it toggled ON saw all the edits I made go through perfectly, with no visible signs of mismatched skin color.

Cntrl f4 also creates a nif file... Strange.
I assume this file is needed? Does the upload to steam funcionality included the dds and this nif automatically?
Quite important as any npc face changes will need all of these.

I think i need some help with this.
Whatever i try to do, either it wont save the dds and tga, or despite it being there, it will still show the mismatch
Also, when you said convert to esm via TesVsnip, did you mean to save it as esm or to make it an esm via the spells ? Doing so via the spells function will fail due to some tes4 error..
What about the "Npc Records" ? Just the npc entry, nothing else ?

Right now i just created my own npc, changed the face values and so on, then i saved it.
Then i convert it to an esm in tesvsnip, load it in the CK again, play around with the lips tone and then finally i try to get the tga and dds files. Now most of the time nothing will happen. It will state, that it was saved, but in reality, nothing was saved. Even if it was saved, the mismatch still occurs in game...
What am i doing wrong?

I think it would greatly help, if you could write a step by step guide..

Maybe, i am just being silly... or maybe just tired

I got my edit to work without the esm change etc. http://skyrim.nexusmods.com/downloads/file.php?id=8331
Just make your changes to the NPC, leave the dialog box, select the NPC in the object window (Under Actors) and hit Cntrl f4. It creates a Nif in meshes, and the dds/tga. The tga is not needed though.

Havent touched tesnip or anything other than the cs.

Which NPC ? A custom one or a stock one ?

Just saw it... you were working on a stock one. As far as i know, this is unproblematic. Its only problematic when it comes to newly created npcs..

Ahh sorry, I missread. I just changed an exsiting npc, sorry.

Perhaps that nif file is the key though? No one has mentioned it yet. If I remove the nif from my mod the colours get screwed up again (And If I leave the nif file there, and only the nif file, default Mjoll's face is the wrong colour with no paint).

Hmm. Ctrl F4 does nothing for me. Is it the same thing using File/Export/Body Part Data?

Edit: Never mind, I was clicking on the character in the render window, not object.

The nif file goes along with the dds. It contains all the headparts, what FaceGen options were used for that npc, and references to the textures used.

During the beta phase, I attempted various ways of exploiting this for an esp-added NPC. But because of how formids work, the first two numbers relate to that mods' load order, it doesn't work.

I have a weird thing where if I copy an npc I can't view the copy in the preview pain. Any race has this error. Sigh.

I managed to do it now Got a custom npc with proper face textures and lip color ! Now all is left is to find out how to add dirt layers. If it works the same way like with lip color, then i dont think
i can do this.

My method is for creating new NPCs from scratch, while Joel's was for editing a pre-existing one. The bottom line seems to be that you can only get working faces if the NPCs are in a .esm file - either Skyrim.esm or your own - and you export the textures with the CTRL+F4 method.

@akbaa: The reason I suggested putting just the NPCs in the .esm file is because converting from .esp to .esm is a pain, and so you can do the bulk of your mod in a .esp file as normal and only need the .esm to hold the NPCs.

HOW?!

I created an npc with all the relevant changes.
Next i opened it with TesVSnip and saved it as an esm.
Then open that (semi) .esm with the CK, make some change (and undo it) and then save it. Now it is a true .esm. Close the CK.
Reopen the CK and load that .esm again, change your npc′s lipcolor to something really extreme (doesnt matter, as lip color currently doesnt show anyway) and set the interpolarity to 1.0.
Click on ok and then select the npc in your object window and press Control + F4. This should create your npc′s facegen data.
Even when you use an .esp now to make further changes, the face will always get showed properly

I hope this helps you and others...at least until Bethesda has fixed this. While you are at it, please also fix dirt and lip color
(and someone please tell me how to make followers go into sandboxing mode instead of waiting mode )

Incorrect, just to let people know. I was experiencing the same issue when editing the face of a stock NPC.

Noticed it later too, apparently you still need to select some crazy lip color and change the interpolation...

Never mind.

Is there a simple fix for this yet? I tried making my new NPC an ESM and doing the export thing, but absolutely nothing happens when I press ctrl-F4. Why is this so damn complicated?!

Didn't change a thing. :\

In the process of making a new companion and this is the only thing really holding me back which is sadness. Hope to get a fix for this soon as this effects all new npc's.

So is this also connected to my issue of creating a race from one of the other races but not being able to preview it? Such a weird set of errors lately.

Is it possible to import a skin from a race in Oblivion into Skyrim?