That is the expected behaviour. The file size of the book is recorded in the database. If the books file does not match that, the device assumes it is a new book, removes all details from the database and processes the book as a new book. And that would also mean it gets the metadata from the new copy of the book.
If you sent the book using calibre, the driver updates the file size during the send. That prevents the book from being reprocessed. But, it is only a good idea if you don't change the structure of the book. As long as the internal files and the TOC don't change, it will be OK.
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