Remove any stems and caps from the chipotle and ancho peppers. Place the peppers into a heatproof bowl, pour in the boiling water and cover the bowl tightly with plastic wrap. Leave the bowl on the counter and let the peppers rehydrate for 30 minutes.
Use tongs to move the ancho chiles into a blender. Ladle some of the soaking liquid into the blender, fix the lid in place and blend on high until smooth. Pour the contents of the blender into a stainless steel stockpot or preserving pot. Use tongs to transfer the soaked chipotle peppers into the pot. Pour the soaking water through a fine mesh sieve into the pot to filter out any particles that fell to the bottom.
Add the remaining ingredients to the pot and bring to a boil, stirring frequently. Reduce the heat to medium-low and simmer for at least 30 minutes, stirring very frequently to prevent scorching, or until the sauce is reduced by more than half and is as thick as ketchup.
Ladle into jars, leaving ½ inch (13 mm) of headspace. Dampen a paper towel with vinegar and use it to wipe the rims. Fasten the lids in place and tighten them appropriately.
Use canning tongs to transfer the jars to a canner filled with enough boiling water to cover the jars by 2 inches (5 cm). Put the lid in place and return to a full rolling boil. Process jars for 15 minutes, adjusting for altitude; see notes below.
Transfer jars to a wire rack or towel-lined counter. Cool completely (at least 12 hours) before removing any rings, wiping clean and labeling. Store in a cool, dark place for up to 1 year.