Rinse beans thoroughly, pick through and discard stones, then set beans aside.
Place ham hocks in a large pot. Add 1 onion, thyme, and salt and pepper. Cover with water and bring to a boil over high heat. Reduce heat to medium-low and simmer, partially covered, for 2 hours. Remove from heat, allow to cool for 15 minutes, then drain ham hocks, discarding onion and thyme. Cut meat from each hock into 2 pieces. Discard bones and set meat aside.
Meanwhile, place pork rind, ham bone, and 1 onion in a large, heavy-bottomed pot. Cook over medium heat, stirring frequently, until pork rind is rendered, about 20 minutes. Add beans and enough water to cover by 1⁄2" (about 8 cups) and season with salt. Bring to a simmer, then reduce heat to low and cook until beans are tender, about 45 minutes. Adjust salt, if necessary, then set beans aside to cool.
Heat duck fat in a large skillet over medium-high heat. Add sausages and cook, turning to brown on all sides, for about 10 minutes. Place garlic, remaining onion, and 1⁄2 cup water in a blender and purée until smooth. Add garlic paste to sausages and reduce heat to medium-low. Cook, turning sausages occasionally, for 10 minutes more.
Preheat oven to 350°. Using a slotted spoon, remove and discard ham bone and onion from beans (it is okay if some pieces of onion remain). Using a slotted spoon, transfer about half the beans with pork rind to a heavy wide-mouthed 5–6 qt. cast-iron, clay, or earthenware pot, about 4" high. Assemble cassoulet in layers: Place the meat from the ham hocks on top of the beans and cover with sausages and garlic paste. Divide duck into 8 pieces by separating drumsticks from thighs and, if using a whole duck, splitting breasts in half crosswise through the bone. Arrange duck on sausages, then spoon in remaining beans with pork rind. Season with nutmeg and add just enough reserved bean cooking liquid to cover the beans (about 3 cups). Reserve remaining liquid. Bake, uncovered, until cassoulet comes to a simmer and a crust begins to form, about 1 hour.
Reduce heat to 250° and cook for 3 hours, checking every hour or so to make sure cassoulet is barely simmering (a little liquid should be bubbling around edges of cassoulet). If cassoulet appears dry, break crust (browned top layer) by gently pushing it down with the back of a spoon, allowing a new layer of beans to rise to the surface. Add just enough reserved bean cooking liquid (or water) to moisten beans.
Remove cassoulet from oven. Allow to cool completely, then cover with a lid or aluminum foil and refrigerate overnight.
Remove cassoulet from refrigerator and allow to warm to room temperature for at least 45 minutes. Meanwhile, preheat oven to 350°. Bake for 1 hour. When cassoulet begins to simmer, break crust and add enough warm water to just cover beans (about 1 cup). Reduce heat to 250° and bake, breaking crust and adding water as needed, for 3 hours. Remove cassoulet from oven and allow to rest for 15–20 minutes. Serve cassoulet from the pot, breaking the crust at the table.