Quote:
Originally Posted by muggleMode
Perhaps a solution would be to save the book folder on the PC in case this happens.
or maybe mark a file in the folder as read-only. 
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A better solution would be to use the Reading List plugin. It can automatically mark which books are on your device. Then if you do have books removed, you can mark all of the book you had on your Reader to be added back again using Reading List. Then you plug in the Reader and the books get put on automatically. It works well once configured.