This happens to me waaaay too much for simple changes (not removing spreads with bookmarks like you mentioned), like making text edits. I've been aware of this since day one of this feature being "released."
When updating links, I always:
- make sure to save my document before publishing changes
- ensure nothing resource-intensive is going on in the background (on computer in general)
- ensure that my internet connection is working
- double and triple-check that my internet connection is working
- Click the update button
- Wait for the wheels to stop spinning before touching anything (this is crucial)
- Save the document again after changes are made (if it is successful)
(Yes I have a modern computer with a stable release of ID)
I usually have a 60% success rate when updating share-for-review docs. I once contacted Adobe phone support and it was pretty clear that they were aware of this yet tried to turn it on "user error" and could not come up with any solutions besides "unshare and reshare," despite mentioning several times that there is a comment history that will be lost if I proceed with their suggestion.
My company pays way too much money to them for this issue to be effectively ignored for two years now. Whenever I'm working with stakeholders who need to review critical documents, I always feel like I have to walk on eggshells and frame it up that "there's a chance that we may lose all of our comments and I'll have to send a new link," which of course always goes over well.
I really like that there are a lot of challenger apps becoming more available on the market so we won't have to rely on Adobe much further.