I am using the bpy.ops.export_scene.fbx operator and it works perfectly, but I was wondering if I am able to use the material overwrite for the export?
So I made a work around. The key was saving the original material, assigning the overwrite material, then reapplying the original. You will need to change the settings for the fbx export click here for its structure.
fbxs = [ ob for ob in bpy.context.selected_objects] bpy.ops.object.select_all(action='DESELECT') for ob in fbxs: ob.select_set(True) mat = bpy.data.materials['Overwrite'] original_mat = ob.data.materials ob.data.materials = mat bpy.ops.export_scene.fbx(...) ob.data.materials = original_mat bpy.ops.object.select_all(action='DESELECT')