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Hi Nihon,
your question might be better asked in the Calibre forum, but here is what I know.
When you add a book to Calibre, it creates its own copy in a file structure that you can't mess with. Converting the book to PDF or MOBI or any other format just adds the new format to this folder.
I don't think there is a way to use Calibre to convert a book without adding it to Calibre's database first.
You can delete the original copy of the book, or consider it as a safety net in case of problems.
Liz
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