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when I edited the titles & authors of books, sometimes the files on the kindle were not recognized as coming from the library. Therefore in the library view, with device connected, the book was shown as not present on the kindle.
I'm not sure how it's called in english, but when I right-click a book on the device in calibre (from the device view) I have an option that will re-sync the copy on the kindle with the copy in the library.
This results in the library (library view) showing correctly that the book is currently present on the kindle.
the other option is "metadata cache update" or something like that in the device drop down menu
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