Preheat the oven to 200 degrees. Using the large holes on a box grater or the grater function of your food processor, grate sweet potatoes and onion.
Crack eggs into a large bowl and beat lightly. Add grated vegetables, flour, thyme, salt and a few grinds of pepper. Stir to combine.
Heat 3 tablespoons of olive oil in a large nonstick skillet over medium heat until shimmering. Add ¼ cup of mixture to the pan at a time, pressing down slightly with the back of the measuring cup to flatten into ½-¾ inch thick cakes. You should be able to fit 6 cakes in the skillet at a time. Cook until golden brown, crisp and cooked through, about 8 minutes total, flipping cakes occasionally. Lower the heat as necessary if the cakes are browning too quickly.
Transfer to a rimmed baking sheet lined with paper towels. Sprinkle with sea salt flakes and transfer to the oven to keep warm.
Wipe out the skillet with a damp paper towel and add the remaining 3 tablespoons of olive oil. Repeat the process with the remaining mixture.