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Those notes are pasted as rich text, so they have their own styles. That's why changing the default size doesn't affect them. You can clear the styles from those notes, but it's a bit tedious. Here's how:
  1. Select the entire text of the note.
  2. Cut the text (Edit → Cut, or Cmd-X)
  3. Press up arrow to leave the text field. This causes OF to treat the note as empty and forget any custom style there.
  4. Add a note back to the item (Cmd-' or click the note icon)
  5. Paste and Match Style to add the note text back (Cmd-Option-Shift V or choose from the Edit menu)