Preheat oven to 400 degrees F. Cover a cookie sheet in aluminum foil.
Cover the cut sides of the butternut squash with 1/2 Tbs olive oil, a pinch of salt, a pinch of pepper, 1/2 tsp thyme, and 1/2 tsp rubbed sage. Place the squash face down (cut sides down) on the cookie sheet. Add the garlic cloves and shallot to the pan and cover in olive oil. Bake in the oven for 40-45 minutes, until soft ( the time it takes to soften depends on how thick it is). Set aside to cool.
Add 4 cups of bone broth, 1/8 tsp cumin, 1/4 tsp nutmeg, 1 tsp salt, 1/4 tsp ground pepper, 1/2 tsp dried thyme, ½ tsp rubbed sage and 1 Tbs honey to a large soup pan.
Remove the butternut squash peel, and cut the butternut squash into cubes. Add the roasted squash, garlic and shallot to the soup pan. Bring the soup to a simmer and cook for 10 minutes. Remove from heat.
Add the cottage cheese to the pan, then puree the soup using an immersion blender OR put all of the ingredient's into a blender. Mix until smooth.