Mix apple slices with lemon juice in a large bowl to coat apple slices in juice.
Stir water, honey, and maple syrup together in a large pot over medium heat until the honey and syrup are melted into the water; add vanilla bean contents and stir. Mix cornstarch, cinnamon, salt, and nutmeg together in a small bowl; stir into the water to dissolve. Bring the mixture to a boil and cook, stirring constantly, for 2 minutes.
Carefully pour apple slices into the water. Bring water again to a boil, reduce heat to medium-low, cover pot with a lid, and cook at a simmer until apples are tender, 6 to 8 minutes.
Remove pot from heat and remove lid to allow apples to cool to room temperature, at least 30 minutes.