It's not a Notes anime, but Fate/Kaleid 3rei is basically an officially published Notes prequel fanfiction.

The world is being filled with some kind of new element, which kills off living beings as they come in contact with it. And the villains try to change humans into something that can survive in a world filled with that element (probably Notes' Liners).

By the time of Kaleid, huge parts of the world are already devoid of life, and most of Fuyuki seems to be empty, as the world is covered in a nuclear winter. All the strong mage families are also gone.

There's also what seems to be a humanoid Type, and a sword arm.

Also, Extra takes place on a Notes timeline.