@Sid Meier - yep you figured it out, you have to delete the material for it to not appear in the "Set Mesh Order" popup. (that dropdown just lists all PDX materials in the scene)
I don't think having the extra material left over should cause problems with export though, as it'll just get skipped/ignored. But I'll do some testing to be sure.
Deleting a bone is definitely a problem though.
Basically suppose I had two Hair meshes; a_hairback and z_hairfront.
I had these two meshes rigged; but the rig was quite clunky, since I had 4 different "hair styles" and had 1 rig to cover all of them; and I was encountering an issue where the hair animations (and only the hair) were experiencing some major flickering I couldn't quite understand; it was too quick to really know if it was a texturing issue, a deformation issue, etc.
So I deleted the hair bones, then the hair meshes; made *four* separate sets of HairFront and HairBack (Hair1_Front, Hair1_Back, Hair2_Front, Hair2_Back, etc) and four sets of rigs for them (I am currently past the 50 joint limit and now I need to go back and delete 7 bones which is quite annoying, there's no reason not to have 100 bones or 1000 bones as the limit tbh) such that each can be rigged an animated separately. (Basically I use a trick with the UV mappings; I separate the hair textures to four corners of my texture file, so the Hair1 texture will show but the other 3 textures will be transparent/invisible).
However when I go to export, I get the following error: "A vertex was mapped to bone Hair_Lower1.R that is no longer present..." or something along those lines.
I made sure that for every visible mesh no deleted vertex groups remained and re-normalized all. But clicking on "Set Mesh Order" I noticed that a_HairBack and z_HairFront remained in the list.
After figuring out how to delete the materials then I export worked (I had switched every "hair" mesh to a duplicate material except for the ones that needed deleting).
So deleting the material was a work around to the deleting the bone/mesh issue to be clear. If I delete a mesh that has an material attached; it should probably automatically remove that mesh from the export list.