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With regard to ADE and Calibre, I only use ADE for downloading books from the EPUB stores. After that, I import them straight into Calibre (straight from the ADE directory in My Documents), for DRM-removal and whatever I want to do to them. When finished, working, and backed up, I delete the books from the ADE folder. ADE is always empty on my computer, and I don't even register the e-reader, nor manage it with that program. Everything, except downloading from the store, is done using Calibre.
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