It’s been ages since I’ve used Make2D. I remember it working a bit differently: If something was obscured it wouldn’t get generated unless you clicked “show hidden objects”.
What I might do is just check the “show hidden” option and that way I can just delete all the hidden objects (I think I haven’t tried). I was hoping to be able to one-shot it though.
Can you please give an example of what you used to see when run Make2D versus what you are getting now that is different, or appears not to be working?