The behavior sounds like you don't have a Part defined in your library for the mounting holes.
To get an idea of what is going on, you ought to look at the reports (click "Show Report" in the "Process Status" dialog box after you do the Compare/ECO).
If you had to Migrate the schematic, there has been a known issue for a while. If your Mounting holes require connectivity and have a Reference Designator, check the "Forward to PCB" Property in DxDesigner and make sure it is set to "True" for these Mounting Holes. If you have a Decal defined for them, they should be OK after Forward Annotiation or Netlist load.
Pull up the info on your part in the Library Manager. If 'ECO Registered Part' is unchecked it won't transfer from the Logic to Layout. I assume it is the same for DxD... which tool are you using?
The original project was done under PADS 9.3. I just did a "save as" in a new folder to get started with this one.
The MTHOLE part has been modified from the original in the library, to add a silk-screen border for the clearance around the head of a screw. It has the ECO registered box checked.
I think the problem has gone away - not sure what I did that fixed it, but the last time I transferred the netlist, I didn't lose the holes.
Thanks for the assistance.