Quote:
Originally Posted by kovidgoyal
Delete the metadata.calibre file on the device then start calibre, it will now show the metadata from inside the books, but note that doing this means the asociation with books in the calibre library will be lost.
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Thank you very much for the informative answer! 
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It seems with your help, I found a way to solve the problem of meaningful removal of books from e-book using Calibre:
-Copy metadata.calibre from e-book
-Remove metadata.calibre from e-book
-Connect e-book to Calibre
-Delete read books from e-book using
Calibre device screen
-Disconnect e-book from Calibre
-Return metadata.calibre to the e-book from the saved copy
-Connect e-book to Calibre
-Update metadata.calibre on e-book
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WIN! (+
asociation with books in the calibre library will be not lost)
A little troublesome, but meaningful