Quick aside, I tested and publishes my eyelashes mod, and those custom files work fine, but those are applied in the race>tongue slot.
The problem seems to be related to loading hairstyles that use facegen sidecar files from the disc, rather than in the .bsa archive.
So I took a vanilla hairstyle asset (haircurlyF) from the .bsa archive (nif, egms, and dds files), and placed them in the appropriate locations in the \Data\ folder. Checking the result in the GECKs NPC preview window, I see that the hair does not deform.
I then made duplicates of the set of files, prefixing filename each with "1", so there's no match in the .bsa. I then created a new hairstyle, assigned it to a race, and checked the result. Again, no deforming. On the offchance that numerics were a problem, I also tried a prefix of "AA" instead of "1", same problem.
So, going back to the modded hairstyle in question, I used Fallout Mod Manager's BSA creator to create an archive for said asset. Deleted the loose files from the game dir, and put the new .bsa in place. The result is that the hairstyle now works with FaceGen as expected.
EDIT: Forgot to mention that any time I created a new hairstyle I also did Character> Update FaceGen Availability.
Any suggestions to avoid the need for this?
