Add lentils and water to a large saucepan. Bring to a boil, then place lid over top and reduce heat to a simmer and simmer for 15-20 minutes, or until the lentils have absorbed the water and are cooked.
While the lentils are cooking, make the flax egg: stir 1 tbsp flaxseed meal and 2.5 tbsp water together and let sit for 5 minutes.
Next, heat 1 tbsp oil in a skillet over medium heat, then add the onion and garlic and sauté for 2-3 minutes or until the onion is soft. Add the parsley, thyme, red pepper flakes, and salt and stir for 1 more minute; remove from heat and set aside.
Once the lentils are cooked, transfer them to a large bowl and use a potato masher or fork to mash them (this should take 1-2 minutes). Then, add the onion mixture to the bowl and stir to combine. Last, stir in the flax egg, flour, breadcrumbs, and cheese.
Use your hands to form the mixture into 12 meatballs. Add the remaining oil to a skillet, then sauté the meatballs for 3-4 minutes, or until they start browning on the outside. If you're adding sauce, remove the skillet from the heat (or turn heat down to low) and pour the sauce over top.