Okay, small update, I've now done the following:
Disable all kobo plugins in Calibre
Set Calibre in "tweaks" to automatically connect to the E: drive (which is the reader once mounted), on startup
Now, I can connect the reader, mount USB storage and then run Calibre.
It will automatically connect to the E: drive.
If I now use Send to Device, it will save my books and populate the "On Device" column, which it remembers when reconnecting the device / restarting Calibre.
So I think I'm nearly there.
Done: I just have to mount my usb storage automatically when connecting To do: Ejecting the reader when closing calibre
But this is a minor niggle, I could learn not to disconnect it accidentally
