What you describe works for me. The book gets updated, but, the ToC isn't updated. I can then navigate through the ToC for the original chapters. I can only reach the new chapters by paging through the book.
That works for epubs downloaded with FanFicFare. It's been a while since I tried this with a kepub. I would expect them to work, but, the page counts and other things might be wonky.
The workaround I generally recommend is to delete the book and resend it. Or, you can turn off the "Do not treat replacements as new books" option in driver. Then the driver won't update the book size in the database and the device will handle the change but deleting the book from the database and importing it as new. But, you lose reading status, annotations etc. You can use my Kobo Utilities to store and restore the reading status, but that means another connection to the PC.
Of course, that's not what I do.
I have a personal calibre plugin to check and fix the ToC for these types of books, for epubs at least. I've been meaning to clean it up a bit as it was one of the first bits of code I wrote for calibre. I haven't been able to bring myself to look at it
I'll put it on my TODO list to clean it up and add it to the Kobo Utilities plugin. If/When I do, it will be something like "Fix ToC for serial book". It won't be aimed at rebuilding the ToC if a book structure is changed, only extended like FFF does.