Heat 1 tablespoon of the olive oil in a large heavy-bottom pot over medium-high heat until shimmering. Add the onion and celery and season with a sprinkle of salt. Sauté until just translucent, about 3 minutes. Add the garlic and sauté until fragrant, about 2 minutes more.
Add the potatoes, stock, bay leaves, thyme and 1 teaspoon of the salt to the pot. Bring the soup to a boil and reduce to a simmer. Leave the soup to simmer, covered, for 25 minutes.
While the soup is simmering, heat the remaining olive oil in a cast iron skillet over medium heat. Add the fennel seeds and sauté until fragrant, about 2 minutes. Add the apples, pears, demerara sugar, cinnamon and the remaining salt and sauté until the fruit caramelizes and a syrup has formed. This should take about 15 minutes. Remove the pan from the heat and set aside.
Remove the thyme sprigs and bay leaves from the soup pot and transfer the soup to a large food processor. Blitz until smooth. Pour the soup back into the pot and place over low heat. Add the cheese and stir until melted and well-integrated.
Divide the soup between 4 bowls and garnish with a dollop of yogurt, a spoonful of sautéed apples and a sprinkling of pepitas. Serve immediately.