In a larger pot, heat olive oil over medium. Add in onions and saute until the onions become translucent, 4-5 minutes. Stir in rhubarb and continue to cook until rhubarb begins to soften, 3-4 minutes.
Next, add remaining ingredients. I start with 1/2 teaspoon of chipotle and taste at the end to see if I want more heat. Stir and bring sauce to a boil, then reduce to a simmer. Let cook for 10-15 minutes. Rhubarb will begin to break down and sauce will smooth out (although, I left a few chunks of rhubarb.)
For filling, heat lime juice in a skillet over medium-low. Add in garlic and cook for 1 minute. Stir in beans and salt, cooking until beans are hot. Remove the swiss chard stem and shred greens. Stir in to beans and cook for one minute. Chard should barely be starting to wilt.
To assemble enchiladas, spread 1/4 cup the rhubarb sauce in the bottom of an 8x8 pan (or something similar.) Have a warm water bath ready and dip each corn tortilla in the water (or you can dip it in the sauce as well) for 10-15 seconds. Remove and fill with bean mixture then carefully roll. Place seem side down in pan. Repeat with the remaining corn tortillas. I choose to only put cheese on top, but you can also toss cheese in each shell.
Add desired amount of cheese on top and cover with remaining rhubarb sauce. Bake for 20-25 minutes. Cheese should be melted and rhubarb sauce should be bubbling.