[Francois_C]

I also do frequent replaces of a book with an improved version, not twice a month but often twice a day, but I didn't even notice that Calibre had been mended since the time it created a new entry every time you would upload a book without deleting the previous one! So I still remove the previous version before updating with the new one, and I did not think to regret to see it considered new: I only kept in mind the chapter I was reading.
But I never update the metadata either. If the cover has been changed and the old one still appears, I switch off the Kobo off and the new one is displayed at restart.
I never experienced a 2-hour wait (we are avid readers and own three different Kobos), except when I start the Kobo with 200 new books on the SD card at once.
The simplest way to update a slightly modified ebook and keep bookmarks and annotations is to overwrite it directly from the HD to the Kobo without using Calibre nor Kobo utilities! The only risk is that bookmarks may become slightly wrong.