Cook the pasta al dente according to box directions. Set aside.
To a medium skillet with high sides, over medium heat, heat the butter.
Add the onions and garlic and cook until softened and fragrant, about 2-3 minutes.
Add the flour and stir to make a roux.
Add the milk and cook over medium low heat, stirring frequently until the milk bubbles slightly and thickens.
Add the butternut squash, mustard and paprika and cook for an additional 4-5 minutes until they are soft.
Transfer to a blender and puree until smooth. Return the sauce back to the pot over medium low heat and add the cheddar and mozzarella cheese. Cook until the cheese melts. Season with salt and pepper to taste.
Take the sauce off the heat and add to the pasta.
Beat the eggs and quickly mix with the sauce and pasta.
Spray 72 mini muffin tins with nonstick spray (ideally use silicon like these ones). Fill the muffin tins with the mixture and top with flax, hemp hearts and parmesan.
Bake for 15-20 minutes or until golden brown and set in a 350 degree oven.
Serve right away, or transfer to a freezer bag to pull out as easy on the go snacks.