Rinse the soaked navy beans and place them in a large pot. Cover with fresh water and bring to a boil. Reduce heat and simmer for about 1 hour, or until tender.

In a separate pan, sauté the chopped onion and minced garlic until translucent.

Preheat the oven to 325°F (165°C). Drain the cooked beans and add them to a baking dish along with the sautéed vegetables, tomato sauce, water, apple cider vinegar, brown sugar, mustard powder, smoked paprika, salt, and pepper.

Stir everything together and cover the dish with foil. Bake in the preheated oven for 1 hour, then remove the foil and bake for an additional 30 minutes until thickened.