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Are an of the books has a non English file name? I have the problem with Calibre xfered book with unicode file name. They will show up in Calibre and in File Explorer but not on the Sony reader. Some of the book will show up again if you put a English ASCII character in front of the file name i.e. ppp.<unicodename>.lrf. make sure you put a "dot" between the English prefix and the unicode name.
Basically I stp using Calibre because of this.
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