This is also happening if you us your own textures / meshes to create a new armor seems to make all apparel edited invisible. Had a quick look and doesn't seem to have effected weapons.
if that is so, then also behaviours, skeletons etc will also be mismatched in the bsa.. but it still doesn't explain the invisibility of all custom races , (alll of my lovely creatures for the moonpath are now broken).
I have all the skeletons etc in my data folder and stillt they don't show up ingame .
uploaded to steam last night, didn't make a final runthtrough,, and now stuck with a dead mod on the workshop.. not a very happy camper...