In a large stockpot, heat the olive oil over medium heat. Add the bacon, chicken sausage, onion, and bell pepper. Break up the sausage and cook, stirring occasionally until the sausage is no longer pink and the vegetables are tender, about 10 to 12 minutes. Add the garlic and cook for an additional five minutes.
Stir in the Swiss chard, kosher salt, black pepper, red pepper flakes, and rosemary. Don’t be alarmed at the amount of Swiss chard in the soup, it will cook down. Continue cooking over medium heat until the Swiss chard has wilted.
Add 6 cups of the chicken stock, one package of the butternut squash, the cannellini beans, navy beans, Parmesan rind, bay leaves, and the concentrated chicken stock. Partially cover the stockpot and cook for 30 minutes.
Combine ¼ cup flour with the remaining 2 cups chicken stock, mixing to dissolve any lumps. Slowly pour into soup and simmer on medium-low for an additional 20 to 30 minutes.
Add the remaining butternut squash and cook until warmed through.
Ladle up and serve with a sprinkling of Parmesan cheese.