[JimmXinu]

Here's the code I use to force a cover update after updating a book in FanFicFare:

First, I use db.add_format_with_hooks(book_id, options['fileform'], book['outfile'], index_is_id=True) instead of just add_format(). I believe the difference is input plugins being run.

Second, I have code that takes a cover from the ebook, using the first page if there isn't an actual image:

from calibre.ebooks.metadata.meta import get_metadata as calibre_get_metadata

            existingepub = db.format(book_id,'EPUB',index_is_id=True, as_file=True)
            epubmi = calibre_get_metadata(existingepub,'EPUB')
            if epubmi.cover_data[1] is not None:
                try:
                    db.set_cover(book_id, epubmi.cover_data[1])
                except:
                    logger.info("Failed to set_cover, skipping")

Third, there is the code to insure that Calibre is notified about all the updates:

        if len(add_list):
            self.gui.library_view.model().books_added(len(add_list))
            self.gui.library_view.model().refresh_ids(add_ids)

        if len(update_list):
            self.gui.library_view.model().refresh_ids(update_ids)

        current = self.gui.library_view.currentIndex()
        self.gui.library_view.model().current_changed(current, self.previous)
        self.gui.tags_view.recount()

        if self.gui.cover_flow:
            self.gui.cover_flow.dataChanged()

Note that a lot of this is from years ago, so it may not be the most up-to-date way.