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I then tried to use the Kobo software to add back a book purchased from Kobobooks and the same freeze occured(sic). However the Kobo showed the book I added except for the cover.
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Hmmm, this is the first time I've heard of someone having major problems with an official 'KoboBooks' book, especially loaded in through the software. For reference sake, which book was it? Maybe someone else had made the same purchase from Kobo and can provide specific insights.
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Calibre still shows the books that I had added since getting the Kobo as present on the device.
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This is just plain weird... Calibre doesn't have a cache of what books are on the device. It just scans for epub files and reads the metadata (can be disabled) to get the device book list. Can you take a look at the Kobo drive through a file manager and see if the books are still there? (I believe last time I did a factory reset, it didn't actually remove plain epub files I dragged on myself)
Just out of curiosity, when you say "freeze", how long did you wait before resetting? I've loaded on a few books with heavy CSS styles that took over 2-3 minutes to process.