Unfortunately, I had to delete the "My Clippings" file some time ago because it caused some indexing problem (this was guided by Amazon advice), and even more unfortunate the fact that I didn't keep a copy of the file. Ever since then I have been using the Kindle page or Kindle for Mac (or more recently, the Cloud Reader) to access my highlights and notes for the book. In all of these, the notes are now gone. 40-50 hours of work down the drain, the Kindle system really isn't designed for serious reading, it's just too unreliable I think (add to that "canned" replies from India or elsewhere in the world and the "World's Best Service" company's image crumbles).
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