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To make the lime-pickled onions, combine ½ the lime juice and ½ the onions in a small bowl, and season. Leave to pickle for 30 mins.
Meanwhile, heat the olive oil in a saucepan over a medium-high heat. Add the garlic and remaining onions, and season. Cook for 8 mins or until the onions are translucent. Add the spices and chipotle purée, cook for 1 min, then add the beans, stock and remaining lime juice. Simmer for 15 mins, then purée in a blender.
Pour the soup into a clean pan to reheat. Serve with a little of the drained pickled onions, topped with a small drizzle of soured cream and some coriander, and the tortillas on the side.