The only app that I could find that was at all helpful in this area was moon reader. I use the paid version because it also has tts. It does not "sync" anything. but it does allow you to "share" your notes for a particular book or all books to any sharing activated app like evernote or email. I gets all highlights, notes, and bookmarks together. This is the closest I have come to a solution. Please let me know if you find a better answer.
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