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Interestingly enough the book shows on the Kobo (without cover), but when I examined the device directory directly I can't see it.
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This is normal. Books you buy from KoboBooks and load onto the device through the official desktop software are injected directly into the SQlite database. (\.kobo\KoboReader.sqlite)
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Some other books and newspapers that I had added, however do show up on the device drive although they do not show up when trying to access them on the Kobo itself.
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I would guess that one of these files is the source of your problems. Delete them. Then re-add them, 1 by 1 until you discover which one is causing problems. There have been a few people that have reported the same freezing/missing books issues you have, and have narrowed it down to corrupt/funky specific books.
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Calibre shows some, but not all, books that were there before I used the device reset, but doesn't show the Great Reset which the Kobo does.
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This is also completely normal. Calibre does not read the contents of the Kobo SQlite database, which, like I mentioned above, is where books loaded through the desktop app are stored.
One of our members here is working on a device driver for Calibre that can handle the SQlite database, and even selectively remove any of the 100 free included books:
https://www.mobileread.com/forums/showthread.php?t=85226
Be warned, it's still in beta testing, so I would make a copy of the SQlite database file (i indicated the path above) before using this driver.