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That's kind of a headache.
Pushing the last version of a book to calibre is quite easy.
But, making sure the "external" files , and calibre's one, are synced... Ouch ! Well, worses than "sync", because calibre will have only the latest file, and the external folders would have the whole history.
Unless I go for the "don't make any any changes to file with calibre", and just use it for sync to device.
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