Log into the KoboBooks web site and go to your Library.
The libarary has a Purchased tab and an I'm Reading tab.
Be sure all your books are in the I'm Reading tab or they won't download to the desktop application.
If they're missing from the I'm Reading tab, select them all in the Purchased tab and press bookmark. Now they'll copy to the I'm Reading tab and an Update Library from the desktop application will transfer them to the desktop app.
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