Did you save the van body under another name? --- Post updated --- I don't mean that. You have to select the body in-game.
You have to select the body in-game. --- Post updated --- Ah wait you did. I'm blind. --- Post updated --- Can you show me the flexbodies?
I think you would have to change the name in blender and in the flexbodies section to the same (e.g. hatch_bumper_F_van). Otherwise it'll get the vanilla parts.