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Personally, I keep only the liberated books in Calibre. The DRM'd books don't do me much good and I don't want Calibre accidentally sending the wrong version to my reader. I've done that before and it's a hassle to delete it and reload the liberated version.
However, that being said, the originals are still in the Adobe Digital Editions folder for epub and pdf, and in the Kindle for PC folder for Amazon books. I do that "just in case" I need them again or lose the Calibre database.
Hope this helps.
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