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No changes made by a reading app to an ebook will make it back to calibre companion. CC ignores the metadata inside the book, instead getting the metadata from calibre.
You can tell Reading List to send books on a list to a device when that device connects. Instead of sending all books every time, you would add new books to RL's send-to list when you add them to calibre and let it remember for you.
DoctorOhh is correct, we are working on adding a "Read" checkbox to CC to compliment the already-existing read date. There will be a way to sync that checkbox with a calibre yes/no custom column, handling the "changed on both sides" problem probably by saying that changes on calibre win. CC's read date will be connectable to a calibre date-type custom column. I haven't yet decided if this will handle the both-sides problem or whether the CC date will always overwrite the value in calibre. I expect that these features will be part of the next prerelease cycle that I expect will start in November. General availability will depend on feedback from the tests.
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