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On the Kobos, I simply copy the .Kobo and Digital Editions directories to my hard drive.
I generally backup before and after each firmware update, as well as every now and then between.
I generally delete the .kobo/dist, .kobo/kepub, and .kobo/slideshow directories, as I don't really need to back them up.
I also delete the .kobo/stacks, as I don't use shelves.
This pretty much gives me the state of the device as at a particular date.
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