Melt butter in a large pot over medium-high heat. Cook onion in melted butter until softened, about 5 minutes.
Mix coriander, garam masala, cumin, and turmeric with the onion; cook until fragrant, about 1 minute. Stir flour into the onion mixture; cook until the flour darkens, about 1 minute more.
Pour water into the pot. Dissolve bouillon in the water. Add apples and season with salt and freshly ground black pepper. Bring the mixture to a boil, stirring occasionally, reduce heat to medium-low, and simmer until the apples are tender, about 15 minutes.
Stir chutney and lemon juice into the soup; remove pot from heat.
Pour soup into a blender no more than half full. Cover and hold lid in place with a towel. Pulse blender a few times before leaving on to blend. Puree in batches until smooth.
Rinse the pot clean, pour pureed soup into the pot, and heat over medium heat just until it begins to boil. Turn heat off completely. Season soup with salt and pepper. Ladle soup into bowls; top each serving with a dollop of yogurt to serve.