Please allow the hole table to detect the holes on a "folded" surface.
The tool is Sheet Metal>Create>Fold
Currently if you place a hole on a surface (not a punch) and then fold it. Then generate your flat pattern, then place it into your .idw... you won't be able to automatically capture the holes on a flat pattern.
I tested this with both circle cuts and drill holes, it only detects punches and any holes that are not on the folded region.
Example: 
Example Hole Fold Issue.zip