Pressing ctrl-F4 does not do anything
Ok. Step by step.
Make changes to NPC in Actor window.
Click OK. The Actor window closes.
On the Object window, click once on the NPC to highlight it.
Press CTRL+F4
A window pops up asking you to confirm: "Export face gen data for all selected NPCs?
Click Yes.
A little window pops up saying "Done!"
Save plug in.
2 new files will be created in Data\Textures\actors\character\FaceGenData\FaceTint\Skyrim.esm\ , one is a dds, the other a tga. You should be able to delete the tga.
Another file will be created in Data\Meshes\actors\character\FaceGenData\FaceGeom\Skyrim.esm
That works for me every time.