I can't for my life figure out why my hda when in unity spawns a secondary mesh (the one marked by a blue arrow). I only want the bottom one to be generated.
Attached a screenshot and the hda.

That is your instance source object (if you are using instances / packed primitives). Think of it as an intermediate object for quick instancing, and will get removed at build time since its under HDA_Data. Or when you bake it out.

Ah okey, Is there a way to get rid of it? I didn't have it previously and I have other assets without it in my scene?