This was driving me crazy for a while (especially when working for a huge IT corporation…), but eventually I found the answer.

Make sure you follow all instructions to a tee as otherwise it won’t work (it’s a cache bug):

Caution: If you got, in addition to IMAP and/or Exchange notes, sole-locally stored notes or POP3 notes, you have to take care on your own to save them separately! If you do not save them, they will be gone / deleted following this instruction!

  1. Go to ‘System Preferences…‘, ‘Internet accounts‘ and deactivate all ‘Notes‘.
  2. Close Notes app.
  3. Go to finder and click on ‘Macintosh HD/library/caches‘. Drag all the contents of the folder to the trash.
  4. Click on the finder, click ‘Go‘, hold the option key and click on ‘libraries‘ (will not appear if you don’t hold the option key). Go to the folder ‘Cashes‘ again and drag everything in the folder to the trash again.
  5. Click on the finder, click ‘Go‘, hold the option key and click on ‘Library‘ and then on the folder ‘Containers‘. Drag com.apple.notes to the trash.
  6. Restart your computer.
  7. Empty trash.
  8. Open notes again and wait for a while till updating of Notes app is finished.

Cred to Gee for the original solution.

How-to: Getting Exchange notes to sync with Mac Notes.app