For the moment nesting utility ignores non-through holes. We are aware of this limitation but we do have a higher-end solution called TruNest that can handle these situations though.
The only other method I know is to export the flat pattern to DXF and place the non-through geometry on layer 5 and give that layer a special color (in my example below , in red). Nesting utility preserves and shows that layer 5 geometry in the nest without having it actually participate in the nesting process. So in my example the red color would be a clear visual indicator to use a special process for these non-through holes.
Cheers
Bob
Bob Van der Donck
Principal UX designer DMG group