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CC has its own config. Calibre does not look for 3rd party settings ( the original CC developer did work on the Calibre Wireless device side, but that remains generic and not CC specific.)
The Calibre Apple or Android driver puts books where its config says to (within the device allowed rules). See if you can make those line up.
EXCEPT IIRC You must use CC to add or CC's DB does not update. DO NOT MIX the 2 methods
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