For head meshes, due to the requirement of their vertex order and count to stay exactly the same as in the fitting EGM (shape morph) and TRI (facial animation morph) files, you will already be screwed right from the start, if you import or export from or to NIF. This will resort the vertices and you can scrap the EGM and TRI files. (Recreating them currently requires around 80 meshes to be created from scratch, 1 for each morph applied to its fullest and for several of the face parts in conjunction, to then create new EGM and TRI files from these. NifTools im-/export scripts are still missing TRI file support, EGM alone is useless for editing head meshes.)
The way around this is through export from NifSkope into OBJ, then importing this into Blender with the option checked to keep vertex order intact. If you then manage to only use deformations which won't alter the order or count of vertices, thus none of the scripted tools, (also no changes to UV-maps = texture mapping layout), and export into OBJ again with the same option checked, you actually managed to modify the head mesh without breaking it.
Re-rigging is a different story, something I haven't yet tried myself admittedly. There are ways to position and orient the head mesh in Blender so it aligns to the rest of the body and perhaps could be rigged to the skeleton again (something along the lines of not moving in Edit Mode but in Object Mode, similar to what is done to head meshes in NifSkope, so the actual vertices keep their coordinates relative to 0 and the morphs can be applied, but they "appear" to be right on the top of the neck instead of in the center of the scene turned to the side), but never try to "join" it to the upperbody to even out alignment issues at the neckline or anything, as this 100% breaks the vertex order!
I'm sorry I can't be of more help with this.