Drain the jackfruit well in a wire mesh strainer, then squeeze firmly to remove excess brine and break the pieces into shredded, uneven chunks.
Heat olive oil in a wide skillet over medium-high heat. After 90 seconds, when the oil is hot, add the jackfruit in an even layer. Cook for 8 minutes, stirring and flipping every 2 minutes, until lightly golden on multiple sides.
Add the red onion, the garlic, coriander, cumin, and oregano and sauté for another 2 minutes until the onions and garlic are fragrant
Stir in the tomato paste, water, lime juice, and salt. Reduce to medium-low heat and cook for 6 minutes, stirring every 60 seconds, until most of the liquid has reduced. Remove from the heat and set aside.
Place the chipotle peppers, pinto beans, water, tomato paste, and salt in a bowl and combine thoroughly. Remove and mash roughly ¼ of the beans with the back of a spoon and add them back into the bowl of beans.
To make the enchilada sauce, place the chili powder, cumin, coriander, cocoa powder, cinnamon, tomato paste, agave nectar, lime juice, flour, vegetable stock, and salt in a blender and blend until completely smooth.
Pour the sauce into a saucepan and bring to a simmer over medium heat, whisking every 30 seconds or so for 5-6 minutes until thickened enough to coat the back of a spoon. Remove from the heat.
Preheat the oven to 375°F (190°C). Spread ½ cup of the enchilada sauce evenly across the bottom of a 9 x 13-inch baking dish or casserole dish.
Warm the tortillas in a dry skillet over medium heat for 30 seconds per side to make them pliable.
Fill each tortilla with about a ¼ cup portion of the jackfruit meat and beans, roll tightly, and place seam-side down in the baking dish.
Pour the remaining enchilada sauce evenly over the enchiladas and sprinkle the cheese evenly across the top. Cover the dish tightly with foil and bake for 20 minutes.
Remove the foil and bake for 10 additional minutes, until the sauce is bubbling and the cheese is fully melted. Remove from the oven and let stand for 5 minutes before serving. Optionally garnish with cilantro, jalapeño, and red onion.