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Originally Posted by Oolong
For some reason when I view the device (or SD card, listed separately) in Calibre, all the options under 'Remove books' are greyed out, except 'Remove selected books'.
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That is the expected behaviour. All of the options in the delete menu act on the selected books. In the calibre library list, each book can have multiple formats and most of the delete options are about removing one or more of the formats. The top option, the only enable one for the device list, is the only one for removing everything about the book. That is the only valid action for books on the device.
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Repeatedly deciding books were unread. If it was just once I'd assume I got confused and opened the wrong file, but it affected more than one book more than once each. Could be coincidence though, a bug to do with something else.
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That is usually the sign of a corrupted database on the device. It's usually most noticeable after restarting the device. Unless you have a clean backup of the database, the only fix is to recreated it by signing out of your Kobo account on the device.
And yes, I can understand why you described it as "confusing the device".