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The problem is that when the Kobo device first sees a book, it extracts the metadata and ToC from the book and loads it into the internal database. This is then used in the library and when reading the book.
If the book is replaced, the default behaviour of the device is to completely remove the details of the book from the database and import the book as a new book. This would get the new ToC. But, lose the reading status.
Because of this, the default behaviour of the KoboTouch driver when sending a replacement of a book to the device is to make changes in the database to make it look like the book hasn't changed. This works fine if the only changes are things like spelling and styles, but it doesn't work if the structure of the book or the ToC is change.
You can turn this behaviour off in the KoboTouch driver. I added an option for this to the driver earlier in the year. Just turn it off to revert to the Kobo default behaviour.
Alternatively, delete the book from the device before sending the replacement. It doesn't matter whether you use the device or calibre to do the delete.
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