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Originally Posted by pauldadams
had to do a copy of the Calibre directory to my device to move my books there.
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You didn't have to copy the Calibre directory. You should have done a "save to disk" to a temporary directory on your hard drive, and then copied *that* directory. As polly said, you shouldn't ever even look inside the Calibre Library directory with Windows Explorer. Calibre will keep multiple copies of the same book in the same folder, but these aren't really duplicates - they are just different formats.
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I had multiple sub-directories for the same book just with a different number in parentheses at the end of the directory name.
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The different numbers indicate that you imported the same book more than once. (The number is the ID that Calibre uses to identify a book) Calibre warns you when you try to do this. These are true duplicates. You can get rid of the second copy by deleting it, or if it is a different format from the first copy, by saving the second to disk, deleting it from Calibre and bringing it back as a different format of the first book.
Edit: BTW, I have four Win Mobile Devices, and the newest one can optionally connect through either ActiveSync or as a USB drive to Windows. Calibre can only talk directly to it when it's connected as a USB drive. Windows can only sync to it when connected via ActiveSync. You may want to check the manual for your Win Mobile device to see if it has this feature. It asks me when I first connect the USB cable how I want to connect.