Apple products are amazing when they work as intended. They are so well designed that they become integrated into your life and then you become dependent upon them. So when they fail to work it is source of enormous frustration.

Having lost the ability to sync Notes when iOS 7 came out (using my not-newest iphone 4S), when Notes functionality returned I suddenly had growing number of duplicate copies of essential (i.e. most frequently accessed & edited) note items. I eventually figured out some were “On My Mac”, but I couldn’t figure out what I was missing in the other versions until I could run diff on the command line, or ediff in emacs. Here is the solution I found…

1. Prepare Notes. The back-up proceedure described next saves each note by its title, and notes with identical titles are over-written. Of course the source of the trouble is the duplicates, hence first carefully find duplicates and give them unique names (e.g. with the last modification time, as shown in Apple Notes).
2. Backup your Notes with Notes Exporter, a Mac application written to complement a Notes app Write. Notes Exporter creates a directory filled with text files, one per note. (Note, previously I had recommended Notes Export for HTML export, but this is now (March 2016) no longer available.)
3. Convert backed up HTML files to TXT (or other formats, like RTF). I never knew about textutil, a Mac utility that converts between document file formats. Run it as
   textutil -convert txt *.html
4. Then run diff between the duplicates and see what’s changed. In my case, may of the duplicates were just that, exact duplicates, but some reflected changes that I would have lost.

Hope this helps someone!