The same thing happens to me repeatedly when I'm highlighting PDF's using Books -- every so often, I go back to a PDF and discover multiple pages of my most recent highlights are missing. It saves highlights as you go along, but sometimes for whatever mystery reason, it decides that the version of your PDF from 11:35 is the newest main one, not the one from 11:45.
These problems, of Apple silently overwriting newer content with an older version, have been going on for at least a decade at this point.
And I just don't understand how such a fatal flaw was ever built into the system in the first place, and how it still hasn't been fixed.