As far as updating the book file in Kindle for PC goes, I've discovered that it won't update until the next time you open Kindle for PC. If Kindle for PC is open while you are instructing Manage Your Kindle to send the update, you won't see it -- most of the time. As you mentioned, sometimes after many tries, the updated book will show up. It's much easier to just make sure Kindle for PC is closed when you send the updated file.
I haven't figured out an efficient way to process these updated files either. I read some books on K4PC and some on Kindle and keep all in Calibre. I'm glad if authors are correcting their badly edited books, but I wish they would put more effort into doing that before they put them up for sale. The last time I looked, I had 67 updates! That's a bit ridiculous.