If you are running a mod that changes a vanilla NPC's weight and you have already seen that vanilla NPC in your game, there will be a gap at the neck, because the NPC's vanilla weight is in your game save. But, it will not cause a black face.
The black face bug in SSE is the grey face bug from Oldrim. It is a direct result of the facegeom NIF file containing data that does not exactly match the last plugin in your load order affecting that specific NPC.
You have more than only Lydia mod installed. This can be confusing, because some people release mods that contain NPCs such as Lydia, even though the mod isn't billed as a Lydia replacer. For example, a mod that supposedly only changes Lydia's sandboxing, outfit or fighting style will also contain the vanilla settings for her face (even though the mod maker doesn't know it). If you load it after a mod you downloaded specifically to change Lydia's face, her face will be black, because the last plugin affecting Lydia contains vanilla Lydia face data, but the Lydia facegeom NIF file contains data matching the mod you downloaded to change Lydia's face. Conflict.
Changing NPCs with plugins is like getting pregnant. You can't do it just a little bit. A mod that changes the Lydia record changes all of Lydia, period. It would be possible to get around that for something like her outfit or sandboxing by instead changing the vanilla outfit and AI package records. Lydia's face would then be unchanged, because the Lydia record itself was unchanged, but any NPC that also used Lydia's AI package or Lydia's housecarl outfit would be affected.
You need to have the plugin you want to control Lydia's face loaded after all other plugin's that might affect Lydia. And, the mesh and texture files from that plugin's mod must be in their proper locations and not overwritten by some other mod.
These are Lydia's facegen files. They have to match the plugin that affects Lydia last.
Skyrim Special Edition\Data\meshes\actors\character\facegendata\facegeom\Skyrim.esm\000A2C8E.NIF
Skyrim Special Edition\Data\textures\actors\character\facegendata\facetint\Skyrim.esm\000a2c8e.dds
It might not be something subtle like a mod that supposedly only changes sandboxing or outfits. You may have accidentally or intentionally installed more than one Lydia replacer. For example, if you install Bijin Warmaidens, then Migal's Housecarl Beauties, then QD Characters, you have installed three different Lydia replacers. If QD Characters was installed last and you told it to overwrite files during installation, then the QD Characters plugin must come last in your load order, because the QD Characters facegeom nif files have overwritten previous Lydia nif files.
This becomes a real pain in the ass if you want NPCs from one mod and NPCs from another mod, but both mods contain some of the same NPCs. You must either edit the mod's plugins in SSEedit to compensate, prior to installing, or you must use mods that don't come with so many NPCs inside their plugins.
Migal's Housecarl Beauties is available as single downloads for each housecarl, so if you just want the ones I converted to male but you want to use Lydia from some other mod, you can do it without having to mess with SSEedit.
The Bijin Series for Oldrim comes with a fomod installer that lets you pick and choose which NPCs you want to install, but it does not exist for SSE. Instead, someone posted Bijin All-In-One, which is named appropriately, because it contains all the Bijin NPCs from the three different Bijin mod pages on the old Skyrim Nexus, which is the exact opposite of what you need if you want to mix and match NPCs from different mods.
QD is also All-In-One. So, the reality is that you probably just have to get good with SSEedit, or you have to be more careful about what you install.