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The Paperwhite still uses the mbp file, which is where the notes and highlights are saved. But your best bet is to either use the My Clippings file or use the Kindle for PC or Kindle for Mac to read and save your notes. Getting the mbp file from there is easier than using the Paperwhite. If you are going to go the method of using the My Clippings file, the new notes are stored at the bottom, so as long as the book is named something relevant, it is easy to find the notes and all you want. You could always empty it out or just rename it to something else and a new one will be created, which should make it easier to find the notes you are looking for.
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