What (or where) are you running Calibre on that has no WiFi available?
does the OS support MTP devices (I think it does from what you say)
The scan needs to complete once, to leave the configuration and found-list (metadata.calibre <don't delete or it all happens again)
Once it completes (and still the device is still connected), You should now be able to set a folder level to maintain in the device driver.
This CAN take quite a while the first time, especially with large, well stocked storage
)
You can still Add Books to Calibre, maintain metadata... You just can't send anything or change a setting (the change
might conflict with what is going on
)