Marvin will attempt to sync highlights even if the book changes. If the the book changes, there's a risk that highlights would be restored to the wrong place. Bookmarks and notes shouldn't be a problem.
Reliable syncing is difficult especially since I don't 'own' the underlying cloud sync service (unlike, say, iBooks) so it will take a while. Right now, I'm focusing on improving location sync (making it more accurate).
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