Puree the canned chipotle peppers in adobo sauce. Set aside.
Crack eggs into a bowl and whisk slightly. Season with salt, pepper, and red pepper flakes.
Heat a skillet over medium heat and add butter. Once the skillet is hot, pour in your eggs.
Cook eggs until mostly set but still glossy.
Lay out tortillas on the countertop and spread pureed chipotle peppers on tortillas.
Divide eggs amongst the tortillas. Place the eggs just below center.
Top eggs with beans, salsa, and cheese.
Roll the burritos and set aside, seam side down.
Heat a clean skillet and place burritos, one at a time, in the warm skillet seam side down.
Cook each burrito on all sides until the tortilla is golden brown and crispy.
Cut twelve large pieces of foil (about 18 inches) and twelve slightly smaller pieces of parchment paper (about 16 inches). Place one piece of parchment paper on top of each piece of foil.
Allow burritos to cool slightly, then place them on your prepared foil.
Wrap tightly, label, and freeze.