Here is some information that might help explain what went wrong.
By default the file name used to store each book is derived from the title and author. If you change one of those and resend the book you will essentially be creating a new book on the device. Any reading history or annotations associated with the original are lost.
The "My Clippings" file contains a log of annotations that you have made on that Kindle. It does not contain the actual highlights used by the Kindle. Those are stored in the .sdr folder associated with each book.
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