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If you made the directories yourself, then you did not use calibre to transfer the books. The books on your computer are not the ones you want to put on your Kindle directly.
Plugboards do not change the books on your computer, they make a copy of the book and change some information on it (namely the title in your case) and then push that fresh modified book on your Kindle, leaving the one on computer original.
You do that inside calibre by right clicking on a book and select "send to main memory". Do not use the file explorer to do so.
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