While the meatballs cooks, melt the vegan butter in a large skillet over medium heat.
Add onions and cook until very soft golden, about 25 minutes, stirring often.
Add garlic and cook another minute until fragrant. Add broth and thyme, and season with salt and pepper.
Bring to a boil, then reduce heat and let simmer until slightly thickened, about 10 minutes.
Add meatballs to skillet, cover with remaining cheese.
Cover and let cook until meatballs are warmed through and cheese is melted, about 5 minutes.