I annotate my Kindle books as well. But at least twice now, I've lost all my annotations because the publisher "updates" the book.
I'm sure that problem won't exist forever (and it doesn't exist for titles that are never updated). But it certainly reduces my trust in the platform. Which reduces how much I take advantage of it.
Under Manage Your Content and Devices, Preferences, there is an Automatic Book Updates item which you can turn off. Then if you want you can update books individually, or not.
They do, yeah. As an author I'm desperate to get into a continuous deployment/iteration cycle for books, but the fact that kindle works this way really discourages it.
I'm sure that problem won't exist forever (and it doesn't exist for titles that are never updated). But it certainly reduces my trust in the platform. Which reduces how much I take advantage of it.