Merging 3D Extrusion Layer into Mesh Layer

When I extrude a 3D Layer, it doesn't translate into the entire object's Texture map, and I'd like to merge the Extrusions Layer into the rest of the object, so when I open the Texture Map it is all one texture and easier to draw on.

I can't select the sublayers of the Mesh to merge them, Photoshop will not let me do that.

Suggestions?  Even when exporting as .obj or .dae, anything, it stays the same.

Does Rendering fix this, is that the solution?