Preheat the oven to 425 degrees. Place the chopped squash on a baking sheet and roast for 45 minutes or until soft when pierced with a knife.
Warm the coconut oil in a large pot or dutch oven. Add the mustard seeds, shallot, and ginger, and cook until the seeds begin to pop and are fragrant, about 3 minutes. Add the garam masala and nutmeg, and cook on low for another 2-3 minutes.
Add the carrots, cashews, and coconut. Stir to combine with the spices. Add the water and cinnamon stick, and bring to a boil. Reduce to simmer, and cook on medium-low heat for about 25 minutes, or until the carrots are soft when pierced with a knife.
When the squash is done, add it to the pot with the carrots. Discard the cinnamon stick. Blitz with an immersion blender until creamy.
Place a scoop of soup into a small bowl and stir with the miso. Return to the pot, add the apple cider vinegar, and stir to combine. Serve with additional coconut and flaky salt, as desired.