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I delete them from the Reader - unless I need to refer to them, such as for a discussion - in that case I delete them later, rather than immediately.
I mainly use calibre to manage books for the Sony Reader. I can't really use it for the DR1000, and I don't need it to get books on Stanza on the Touch. My main ebook library is just folders on my HD (and backed up somewhere else) - I de-DRM everything as soon as I have bought and downloaded it, so I can do whatever I need with the files.
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