My guess from this is that while the device was full, something happened to either corrupt the database, or get it out of sync with what is actually on the device. It is possible that has fixed itself, and that tapping a book on the device will download it using WiFi. Or trigger it to be downloaded the next time you connect to the computer and run the desktop application.
You could just do this and check if the books are downloaded correctly. But, I think I would do a little preventative maintenance. I would suggest that you sign out of the Kobo account on the device and then sign back in. What this will do is clear all the downloaded books, remove their covers from the device and generate a new database. Then it will download the details of the books and actually download the books for five of them. I you do the setup using the desktop application all books will be downloaded to the device until it gets nearly full. But, you can skip this and choose which books you want to send to the device.
If you are worried about the state of the library in the desktop, you can also rebuild that by signing out of your Kobo account on it. If I was doing this, I would backup the directory with the library in it first. The directory is different for Windows and Mac and I can't remember exactly where it is for either at the moment, and I can't check.
If the above doesn't work, there is the more drastic step of doing a factory reset. This will completely wipe the device back to the out of factory state. Then you do the setup using either WiFi or the desktop application.
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