The annotations syncing between the devices and apps haven't been working properly for a while. They tend to sync once or maybe twice for a book, but, after that, they don't. It's possible that they sync from one place to the other until you open the book on the second place. I'm not sure of that as I never r I suspect it is something in the tracking of what is on each device that is being messed up. I doubt very much that the export function is having an affect.
I know Kobo are aware of the problem, and should be working on it. But, I recommend reporting it so that they know how many people are affected.
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