Whisk together the lemon juice and 2 tablespoons of the oil in a large bowl; season with salt and black pepper. Add the chicken, toss well and set aside at room temperature for 15 minutes.
Drain the chicken and pat dry. Heat a wok or large skillet over high heat. Add the remaining 2 tablespoons oil and then the chicken and thyme. Cook, stirring until just cooked through, about 4 minutes. Use a slotted spoon to transfer the mixture to a large bowl. Add the bell pepper to the pan and quickly cook, stirring, until softened, 1 to 2 minutes. Transfer the bell pepper to the bowl with the chicken. Add the zucchini to the pan and cook, stirring, until crisp-tender, about 2 minutes. Transfer to the bowl with the chicken. Add the tomatoes, garlic, scallions and red pepper flakes to the pan and cook, stirring, until lightly browned, about 2 minutes more. Return the chicken and vegetables to the pan; season with salt and black pepper. Cook, stirring, until well combined and warmed through, about 2 minutes.
Remove from the heat and stir in the basil. Serve over rice.
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