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Open your "Path to your WoW folder\WTF\Account\ACCOUNT NAME\SavedVariables\" folder, and find the "Carbonite.lua" file. Open it with any plain text editor and do a search within the document for "NXFav". There are several instances of that phrase, but the one you're looking for will be almost all the way at the bottom of the document, and will be the last occurrence of it. You will (probably) recognize the notes several lines below it.
If your notes are still in the file, I would have no idea why they aren't showing up. I think somewhere in Carbonites options they can be enabled/disabled, so they possibly got accidentally disabled.
As far as I know, if your notes are no longer in that file, unless you have a recent backup of it there is no way to recover them. If you do, indeed, have a recent backup, it may be possible to copy the notes out of it, and paste them in the current file at the proper location.
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