I like Emmanual's suggestion.
Forming the structure as Calibre itself does in the Cybook would help a lot. Likewise a longer list of I/O filters may help as the metadata transfer does leave a lot of tidying up sometimes.
ie if in Calibre I change the title in the Library, it isn't transferred to the Cybook, I have to re-do it on the Cybook. It then gives an error, but changes it anyway.
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