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the database should be in the library folder. I am not sure about why the size what it is. Guess that you have converted ebooks from on version to another this will make copies of the files in the library that calibre is using. Also you said that you have made lots of changes to the metadata that is also stored. And I believe that it also stores images of the book covers separately.
I hope someone else has a better explaination.
chuck
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