Thanks for submitting a support ticket. When converting Gerber to Drill, FAB 3000 uses "Flashed pads" only. The large non plated holes are drawn as Polygons (you can move the mouse over to show the object type), which is why it's ignored during Gerber to Drill conversion. This example tutorial shows exactly how to ensure you have flashed pads and then convert to drill:
Note: The reason the Drill imports weirdly, is that Drill data does not contain the Integer and Decimal digits. When you're exporting the drill file, keep in mind the Integer and Decimal digits -- then when importing back into FAB 3000 or any other tool use those same settings.
Note: To ensure the "easiest" export quality, select "Decimal" for Zero Suppression. See below:
Let me know if that helps.