You could also check and edit the formatting before you send the book to your Kobo in the first place, but few people want to bother with that.
I do edit my books before, but sometimes I still notice something I want to fix while reading. I delete the book using Calibre (not directly from Kobo) and send the new version. I also have "Do not treat..." permanently unchecked, but then I don't bookmark, highlight or annotate, and I'm fine with finding my reading position manually.
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