I'm just going to hazard a guess as to what is causing the problem, as it is somewhat long, I'm going to put a spoiler tab to save space.
Spoiler:
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The Apachii hair mod is probably minorly conflicting by changing what number her hair is, so the hair looks like that because the game doesn't know how to handle it. Something like this happened to me when I switched a hair mod to a merged plugin, it changed my character to being bald, in spite of the fact that the hairstyle he was using is still in the game. The way I fixed it was going into the racemenu to change my hair back to the way it was supposed to be. That worked because I was the player however. I'm not as sure how to fix an npc's hair. If I had to guess, a compatibility patch would have to be made by using the apachii hair mod as a master, changing the npc in the creation kit, and keeping apachii as a master for the plugin would likely fix the issue. I believe the instructions on how to do so are here. https://www.nexusmods.com/skyrim/mods/15411/?
Of course, this is all a bunch of guesses, so I could be completely wrong. Still thought it would be a good idea to mention this.
I'm having this problem also. There is no hood, she doesn't have a hood in my game. The only way I could fix this was managing her outfits with AFT, but then I lose her beautiful green eyes! (the fix for that given in the description doesn't work for me). It's really annoying that I can't have both, green eyes and lovely hairdo!
The .esp is still in Form 43 (Oldrim) format. Tools like Wrye Bash are now Form 44-enforcing, meaning they will throw errors/warnings regarding plug-ins not being properly converted to Form 44 (Skyrim SE) format. Failure to properly convert Oldrim plug-ins using the Skyrim SE CK can/will lead to weird in-game behavior/CTDs/freezes/save game corruption due to duplicate Form IDs being loaded into one's save game. Further details as to why all Skyrim SE plug-ins must be converted to Form 44 (Skyrim SE) can be found here:
I think i figured this one out. I use True Eyes for my eye mod. for some reason, it conflicts with this mod and caused Serana's face to turn brown. Added either the Iridium or Original eyes file from the optional section and it seemed to fix the issue. No more "Brown Face"
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http://litewolf.altervista.org/immagini/serana.jpg
The Apachii hair mod is probably minorly conflicting by changing what number her hair is, so the hair looks like that because the game doesn't know how to handle it. Something like this happened to me when I switched a hair mod to a merged plugin, it changed my character to being bald, in spite of the fact that the hairstyle he was using is still in the game. The way I fixed it was going into the racemenu to change my hair back to the way it was supposed to be. That worked because I was the player however. I'm not as sure how to fix an npc's hair. If I had to guess, a compatibility patch would have to be made by using the apachii hair mod as a master, changing the npc in the creation kit, and keeping apachii as a master for the plugin would likely fix the issue. I believe the instructions on how to do so are here.
https://www.nexusmods.com/skyrim/mods/15411/?
Of course, this is all a bunch of guesses, so I could be completely wrong. Still thought it would be a good idea to mention this.
https://afkmods.iguanadons.net/index.php?/topic/4633-skyrim-se-things-to-know-when-converting-standard-mods-to-sse/
Many thanks!!