I archive all my ebooks on a server for safety's sake. When I load books on my Sony 650, I check to make sure they loaded correctly then I delete them from Calibre.
When I finish reading, I delete from the Sony.
BUT ... I use a app for my iPod touch called "Book Crawler" to track what I have read. The app does a wonderful job of highlighting unread books and because I always have my touch with me if someone mentions a book, I quickly enter it into the database and mark it unread.
For me ... this all works great. No fuss, no clutter.
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