When you say you want the new one, you are NOT telling calibre "use the new version", you are saying "yes I know it's already here, add the new book record anyway".
Books are matched like this: when a book is sent from calibre, the calibre metadata is used to record the book in the file %KINDLEDRIVE%\metadata.calibre
If calibre senses the book when connecting your device, but it's not in the metadata.calibre, it will read the file and extract some basic info.
Once the metadata.calibre is updated (the first thing calibre does when you connect your device) it attempts to match books to your library; it does this by comparing the title registered in metadata.calibre to the one in the calibre database. If the titles aren't exactly the same, you don't get a check mark.
If the book record had the title changed, for instance you merge the two records together, then it may no longer match the record in the metadata.calibre, depending on how the book was indexed in the metadata.calibre, what the current title is there, and what the calibre record says.
You could send the book from calibre, and then it will match up. I always do this just so the plugboard title gets updated.
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