I have had a look at the database. It is weird.
From most of the dates, you did a factory reset on the 22nd. That agrees with the post.
But the shelves are what are strange. There is a set with timestamps around 2013-06-09T18:31:31Z. Then there is another set with timestamps from before this. The timestamps for these range over several months, so they are probably the ones that should be there.
The theory I wanted to check was that the shelves didn't sync from the Kobo server after the factory reset. Then, you connected to calibre and it created a set of shelves. After that, you did a Kobo sync that recreated the shelves you had before.
That could end up with duplicate shelves as the sync to Kobo is based on an id rather than just the name. But, because of the timestamps, that doesn't work. Unless the clock on your computer had the wrong date.
So, I don't know what happened.
I'm not sure, but I think if you do a sync, the shelves you deleted from the database will come back. If they do, change the value of "_IsDeleted" to "true" for the ones you want to get rid of. With that, the duplicates should disappear on the device. At the next sync the rows should be removed from the database and the server.
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