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Don't touch calibre's private files (read my .sig for details).
If you want to put your ebooks, of any/whatever format, into a single folder, use "Save as..." (which should be called "export") to do that. Then you can put them wherever you want, and do whatever you want with them. But calibre's internal files are its own, and should not be messed with. Just pretend they're a black box.
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