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there is a remote possibility the mod changes have become a permanent part of your save game. The only fix might be as stated in post #18
Things that are mod dependent and can break saved games are things like modded in objects, weapons, clothes... and you are storing those in any chest or on your person.
Odds are that if the folders
data\textures\actors\character\basehumanfemale
data\meshes\actors\character\characterassets
Have been removed and the files verified and the problem persists either they missed a ba2\esp file related to the mod or it somehow did what we believe should not be possible and somehow it did become part of the save. Unless there is an outside chance of the mod somehow installing the files somewhere else however the esp\esl files would still have to be activated to load them if they are not simply replacing the base game files with a new one of the same name. If we knew the mod name perhaps we could point to the exact file causing the issue.
There is actually a lot of pictures of distorted npcs from people who removed body replacement mods or skeleton replacement mods mid game that suggest otherwise.
Once such mods are fully removed and game is verified, load up saved game, save another one. Then restart the game and load that new save. Problem solved.
i don't have that installed
However if you do install it then it will replace the files that cause them to be nude with a non nude version then you can uninstall that mod and see if the problem remains resolved.
CBBE is the only mod I know that gives you an option of non-nude. If all the armor mods are CBBE then no NPC will be nude... regardless of whatever other bodies you have installed, overwrite them with Caliente's mod. (https://www.nexusmods.com/fallout4/mods/20656)
(unless you absolutely sure it is ok but even then)
If you haven't done it already OP I suggest to start a new game and see if the issue is still there.
If you downloaded loose files - they don't get "deactivated" - they stay inside the mod folder.
You want to properly remove them you need to delete your data texture folder then verify files. Or if you have big download speed delete data folder and verify files.