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Preheat oven to 350°F with rack in the middle. Cut apples into eights and cut out core and seeds.
Combine the apples, water, salt, lemon, vanilla, and cinnamon in a wide, ovenproof pan. Cook, covered, over medium-high heat, stirring occasionally, until the apples are soft and collapsing, 30-40 minutes.
Carefully transfer the apples to a food processor, in batches if necessary, and pulse until smooth. Transfer the puree back to the pan, stir, and then place in the oven. Bake, stirring regularly, every 15 minutes or so, until the apple butter is thick and concentrated - another hour or two. I typically taste for sweetness before placing in the oven and add the brown sugar if needed. The apple butter you see pictured here was in the oven for about 90 minutes, but you might go longer if you want it thicker and even more concentrated. Your spoon should leave a trail across the bottom when it’s done. Allow it to cool a bit and then stir in the miso. Taste and adjust with more salt or lemon juice if needed.
Refrigerate for up to two weeks or freeze for up to six months.