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This is something calibre might need a function for, actually. If I have 2,000 files on my Reader and 2,001 in calibre, a title-by-title comparison to find the difference isn't all that practical. Not for a human. Calibre gets the device file data already, so putting a little check mark next to files in the library that are on the device (with maybe a distinction between main memory and card, if applicable) when it's connected would make life a bit easier. That could also be incorporated into a "don't try to transfer a file if it's already there" option.
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