Cook pasta shells according to package directions, al dente.
Melt butter, add onion and cook until tender. Stir in flour, bouillon, garlic salt, thyme and pepper.
Cook until mixture thickens, stirring constantly. Whisk in milk and stir until hot. Stir in cottage cheese, broccoli, cooked chicken and cheese. Allow to cool slightly, will thicken.
Fill large shells and top with more cheddar cheese. Bake at 350 degrees for about 20-25 minutes or until bubbly.