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@Carlos_ER: That's a "feature" of the Kobo devices.
When the Kobo device first sees a book, it processes it and adds it to the internal database. The information stored includes the title and author and some other metadata, the file size and the TOC. This database is used for the library lists. And the stored TOC is used for navigation when reading.
Unfortunately when you replace a book, it isn't reprocessed. In fact, if the files size changes, the device deletes the book and removes it from the database. The KoboTouch driver in calibre modifies the stored file size so that this doesn't happen. But, there is no way to get the book reprocessed to update the metadata and the TOC. To do that, you need to delete the book from the device, and then send it as a new book. This will mean the loss of the current reading position and any annotations or bookmarks.
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