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Yes, you need to be careful when bringing books over to Calibre to only bring the actual book files.
Every book on the kindle that has been read or examined will have two files: one the book itself, the other containing annotations, highlights, last page read, etc. Most of these files will have identical names with different filetypes.
An Amazon book might have files like: "great book.azw" and "great book.mbp". Pdf books might have files like: "great pdf book.pdf" and "great pdf book.pdr".
On Calibre you would want the .azw, and .pdf files, but not the others.
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