Thanks for your time. As I wasn't 100% sure, I downloaded again from Kicad (not the kicad.github.io,
the "if you cannot wait"...).
I could observe that the file has been changed 13 hours ago, which corresponds more or less to
the time you did it (yesterday night in Japan time).
Summary of what I did:
1. Download (see above)
2. Remove the lib Mounting holes from the pcb_new menu-> footprint library manager
3. Remove the library physically on the disk, and add the one I have downloaded in (1).
4. Added the new one using the wizard
5. Just in case, opened the schematic, changed all the footprints assignement for the 4 hole items
6. Exported the net list
7. Imported the net list from the layout editor
Result: the air wires are still here. I pushed B just in case, to refresh the drawing.
Is there anything wrong in this sequence?