Bring a large pot of salted water to a boil.
Lay the sardines on a paper towel and, working one at a time, use a sharp paring knife to fillet each fish from head to tail (see the video). Remove and discard the fish bones and reserve the sardine fillets and tomato sauce.
In a large skillet over medium-high heat, add the olive oil and garlic, and cook, stirring often until aromatic, about 2 minutes. Add 2 teaspoons of the Espelette and continue to cook until the garlic is soft and translucent (without browning), 2 minutes more. Stir in the chives, half of the sardines and the remaining 1 teaspoon of Espelette; remove from heat and season with a pinch of salt.
Add the pasta to the boiling water and cook until almost al dente, 7 to 8 minutes. Drain and reserve 1 cup of the pasta water.
Add the reserved tomato sauce to the sauté pan and return to medium-high heat. Add the pasta, almonds and dill, and thin out the sauce with ½ cup of pasta water, cooking 1 to 2 minutes. Stir in ¾ of the lemon zest and the remaining sardines. Cook until the sauce is mostly reduced, another 2 to 3 minutes. Taste and adjust the sauce consistency and season with pasta water, salt and lemon juice.
Divide the pasta between 2 bowls and sprinkle the remaining lemon zest over top. Garnish with a pinch of flaky salt and dill, and serve.