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Add the sliced red onions to a medium bowl. Pour enough boiling water over them so that they are covered. Count to 5, then drain. Add the onions to glass jars (or a food-safe glass container with a lid).
Toast the cinnamon sticks, cloves, and pepper flakes until fragrant in a small saucepan over medium heat, 3 to 5 minutes.
Whisk in the apple cider vinegar, lime juice, sugar, and salt.
Bring to a simmer and cook until the sugar and salt have dissolved, 1 to 2 minutes.
Taste the brine for sweetness, and then add more sugar as needed.
Pour the pickle brine over the onions, pushing them down so they are covered. Add the lid and set aside on the counter until cooled.
Refrigerate for 2 to 3 weeks, ensuring the pickled onions stay submerged in the brine.