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The Kobo Touch Extended Driver options, in the Collections, Covers and Uploads tab, at the very bottom, has a check mark option you an turn off called "Do not Treat replacement books as new books". Basically, the Calibre Driver tries to slip a replacement book in place without the Kobo noticing, thus preserving your reading position, bookmarks and annotations. This works if edits are limited to fixing a typo or updating some formatting in the CSS. Unfortunately, as seen here, it will not work if the Table of Contents is changed or if a change is made to how files are split. (and maybe if whole paragraphs are added/removed.)
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