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Since you mention the Kobo Desktop app, this suggests that these are books purchased from Kobo. Your Clara BW will get a list of those books and a download of a relatively small number during setup when you connected it to your Kobo account.
If you go into Books on the Clara BW and tap on the ... in the right hand edge on the same line as Filter and Sort, does it show Download All as an option (not greyed out)? If you tap on Filter, what numbers does it show for All, eBooks, Unread, all the way down to Downloaded?
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