If not sure repeat mod instalation whichever way you do it: manually or mod manager. That files are usually added loosely by CBBE mod, though any other mod that does modifications to the base characters bodies can do that aswell. Your mods won't be affected since they only add files: files that aren't vanilla files are left untouched by Steam integrity checks. If I were you I would do a file integrity check in Steam to ensure you didn't deleted any file you shouldn't. What you have there are loose files that replace vanilla ones if present, if not, then vanilla is used. Files starting with 'DLC' are the vanilla Data for official DLCs of the game(only. ba2 extension starting in 'Fallout4 -' contain the vanilla assests. You don't need male vanilla body files, neither female vanilla. I'm afraid I cannot access your D:\ drive.
