Place beef chuck and pork knuckle in a large pot and cover with cold water. Bring to a boil over high heat, then drain and rinse meat under cold water to remove impurities.

Heat a small pan over medium heat, add annatto seeds and toast for 2 minutes, stirring constantly until fragrant and oil is released.

Pour beef stock into the stockpot with toasted annatto seeds and bring to a boil. Add blanched beef and pork, then reduce heat to low and simmer gently for 15 minutes.

Add bruised lemongrass stalks, minced garlic, halved shallot, dried chilies, and shrimp paste to the broth. Stir until the shrimp paste dissolves.

Simmer broth on low heat for 45 minutes, skimming any foam that rises to the surface to keep the broth clear.

After meat is tender, stir in fish sauce, sugar, and salt to taste, adjusting seasoning as needed.

Cook rice vermicelli noodles according to package directions (3–5 minutes in boiling water). Drain and rinse under cool water to prevent sticking.

Strain the broth through a fine-mesh strainer, discarding lemongrass, shallot, and chilies. Return strained broth and meat to the pot and keep warm.

Divide noodles among bowls, ladle hot broth with beef and pork over top, and garnish with fried shallots, fresh herbs, bean sprouts, lime wedges, chili oil, and sliced pork sausage.