I've had this issue with a Libra 2 on MacOS. I think it might be some kind of timing issue.
The best workaround I have found is to add USB Connect to your menus with Nickelmenu. If I plug in my Kobo and it doesn't show up, this menu option will establish the connection to Calibre.
Code:
menu_item : main : USB Connect : nickel_misc : force_usb_connection
This is also useful to populate your metadata after importing a new book without unplugging and replugging.