I'm probably confused. Pardon my confusion. I thought that there was some sort of exclusion list that calibre would not remove those shelves. Plus the remove shelf checkbox could possibly be set to not remove any shelves.
I've never made shelves on the Kobo as calibre did it flawlessly already when I bought my first Kobo. The Kobo drivers are great. Still if I labored long and hard to make a shelf on the Kobo I might be a bit disappointed if it disappeared, especially if I didn't know how to quickly recreate it using calibre.
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