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If I do a significant change to the book, metadata, etc. I remove the original in favor of the changed version but I do not delete the original. I have a folder I use for such things. I also store all my books in a "master book" folder in three separate locations, a usb stick, separate hard drive and my lap to hard drive in addition to the Calibre library.
I realize this is overkill but I'd hate to lose my books, especially the originals and edited copies.
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