Cut stems and center ribs from Swiss chard, discarding tough areas near the base of stems. Cut stems into 1-inch pieces and tear leaves into 2 or 3 pieces each. Set aside.
Rinse scallops and pat them dry. In a bowl, combine almond flour, garam masala, thyme, and salt. Add scallops and toss to coat. Set aside.
Cook bacon in a large skillet over medium heat until just brown and crispy, about 5 minutes. Use a slotted spoon to transfer bacon to a paper towel-lined plate to drain, reserving the drippings in the skillet. Add scallops to drippings in skillet and cook over medium-high heat, turning once, until browned and opaque, about 6 minutes. Remove scallops from skillet.
Heat olive oil in skillet over medium heat. Add chard stems and garlic and cook, stirring, for 2 minutes. Add chard leaves and water. Cook over medium-high heat, covered, until stems are tender and leaves have wilted, about 2 minutes. Add vinegar and toss to coat evenly. Return scallops and bacon to skillet and cook until just heated through.