I'm using Super High Rez Skin Texture for HGEC by Ozmo and I'm sure it includes lower part.
When I installed it, this happens ;


I also use the underwear version from the normal HGEC texture. The underwear texture works fine but when I remove underwearlower.dds or underwearlower_n.dss, the mesh/texture is ..kinda missing.
Any help here? I've tried removing all the underwear file and overwrite the skin texture but it still looks missing.

OK I don't know if I can help you but I will try if not then others can.
A couple of questions.
1 when you say you removed the underwear texture do you mean delete only or what.
2 Do you use any Programs to install and uninstall these mods. example wyre bash, OMM, Archive Invalidate.

Now the problem may be simple I don't use the Non nvde Textures, but You say you are using the Underwear version of HGEC and you are deleting the underwear, I think they just did not put any genitalia for them and painted it black. Now if you want to see that you must install HGEC nvde to be able to see it. As I said I think that may be the problem, I could be wrong. Good luck

1. There's no non-nvde texture. All body textures contain nudity, even vanilla body textures(If you're wondering about that, unpack upperbody texture and lowerbody texture from BSA and look). So-called 'underwear' version is a body replacer which has overlaying underwear meshes, like normal clothing.
2. Do not delete underwear texture like that, otherwise you will only see purple blobs(missing texture), invisibility(missing normal map) and any other oddities like you've seen. Some underwear body replacer may not have underlying body parts under the clothes.
3. If you want to install other body texture pack, just overwrite newer skin textures over older ones. Deleting part of body replacer does not any help.