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There was an issue with map notes in Carbonite version 3.2, where they were given a massive minus Y value, causing them to appear off the map... or in common terms, "disappeared". This was supposedly fixed in 3.21 though - do you have 3.2, or 3.21? Does it read 3.21 at the top of Carb's options window?
And as I mentioned, all addons save their data - settings, layouts, and in this case, map notes - to the WTF folder. It should still be there if you haven't touched it, regardless of whether you can see the notes or not.
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