I have plugged my Kobo into a computer with Calibre running or started Calibre after the reader is plugged into computer. Checked connect on Kobo screen. Calibre will show books on device (e-reader) and Storage Card A. Select books I want transfered to e-reader by shift left clicking on Calibre list of books on Device or on Storage Card A. I then right click on selected books, causing Calibre pop up menu to show, "Add books to library" that I select. I have transfered from 1 to 2000 books at once this way without problems. Better to transfer fewer books at a time to reader making it easier to find books causing problems on reader.
I also have archived file of all books as down loaded from Internet before transfered into Calibre file system.
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