As far as I know, you can't delete the parts node in Terragen once they've been imported into a scene. I guess the one in the main node window is one you've pasted there as a test.
I just did a quick experiment and edited the .tgd in a text editor: 
Renamed the nodes B46_Void shader and parts node by adding the text "TO_DELETE" in a Terragen scene first
Then searched for those in the .tgd file and deleted these strings :
Quote<default_shader
            name = "B46_Void shader  TO_DELETE"
            (terragen parameter list in between these lines)
            >
         </default_shader>
and: 
Quote<object_part
            name = "B46_Void  TO_DELETE"
            gui_use_node_pos = "1"
            gui_node_pos = "400 180 0"
            gui_group = ""
            part = "B46_Void"
            shader = "B46_Void shader  TO_DELETE"
            >
         </object_part>
So basically the shader code for B46_Void bounded by 
<default_shader (...) </default_shader>And the object part bounded by 
<object_part (...) </object_part>Re-saved to a new .tgd  file and the part is gone, don't how that will affect the scene without seeing the geo though.
I get into the habit now of checking and editing the .mtl file before I  load it into Terragen