The Amazon rep should have told you that automatic book updates is an opt in feature. From your manage content/devices there is in setting a tab for it. But the warning:
Quote:
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Opt in for automatic book updates to receive new versions of your books when we have confirmed that improvements were made. In order to retain your notes, highlights, bookmarks and furthest reading locations, ensure that all your Kindle devices and reading apps have the "Annotation Back Up" setting turned on.
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Is enough for me to not bother to turn it on. I do not use annotation backup or whispersync enabled, because I do not want my wife's annotations or bookmarks when reading same book. Technically a book update is a different book for the Kindle, old gets deleted, new gets downloaded. If the bookmarks and notes changed (different locations) Amazon will translate them, but can only do so on the server stored version. That will also get pushed back to the Kindle.
Maybe having it turned on is not enough unless you initiate a sync by hand?