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I found library management a complete and utter mess (even with Calibre) so now I just copy all my ebooks directly to the ereader and back up the entire ereader drive.
I also have a SD card so back that drive up too.
If you get an automated backup program like (the free) Cobian Backup it should handle it all for you with ease.
Alternatively you can just have a single drive on your PC with all your ebooks in and back that up. I do this anyway so have two backup copies of everything.
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