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Looking at my own set-up Calibre is just copying the whole file for each book plus its own data into another directory I have set up just for Calibre books . Once that is done then I just archive all the original EPUb files I have downloaded, other stuff I have in other directories. I do this archiving about every 2-3 months and just store all the files on a DVD and delete them off my computer. I have a lot of space on my hard drive but really just don't like having a lot of duplicate files and unwanted junk on my computer, no doubt a hang-over from the days of computers with very limited hard disk sizes! This way I also find it easier to back up data files on my computer because files are stored on the secondary D drive rather than the C drive which holds programs and operating data. I am such a computer tidy freak - pity it doesn't carry over to my house!
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