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I have not understood what you are doing, or the result you want.
In calibre, the metadata of a book (e.g. title, author) are stored separately from the book file.
When a book is exported from calibre, the metadata is copied into the saved book file, but the file in calibre is unchanged.
Perhaps you could explain slowly, with numbered steps, what you're doing, clearly identifying the files you're talking about at each stage.
If you have any public domain books in your library, you could even upload copies of one particular book at the various stages.
Perhaps then someone will be able to tell you which bit is going wrong.
From the current description, it's impossible to say.
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