As Peter said, that is the old driver. If, on the "Sending books to device" preference page in calibre, you have "Metadata management" set to automatic, the driver changed the reading status. Firstly, it resets the status to unread. Then it looks at the tags to set the status. If book has "Im_Reading" or "Read" as a tag, the status is set. Personally, I didn't like that, so I never used it. When I rewrote the drive for the 2.0.0 firmware on the Touch, I removed that function.
As to the backup, yes, that would be a good idea in some sort of Kobo Utilities plugin for calibre.
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