If canning, Sterilize the jars by placing them in a 250F oven for 10 minutes. (jars only, not the lids)If you aren't going to can the jars, simply fill them with the onions and hot vinegar mix, then store in the fridge.
Add the vinegar, sugar, and water to a small pot over medium low heat. Bring up to a gentle boil, until the sugar is dissolved. Turn off the heat.
Place the large canning pot on the stove full about 3/4 the way with water. Start bringing up to a boil while you prepare the onions.
Peel the onions, and remove the stem and root ends. Cut in half. Then very thinly slice.
Remove jars from the oven and place on a tea towel on the counter. Fill the three jars with the onion slices, and pack them pretty tight. Divide the 1 tsp of chili flakes between the three jars.
Using a canning funnel, add the hot vinegar mix to each jar, leaving 1/2 an inch of head space at the top. Use a butter knife to poke out any air bubbles from the jars, and top up with vinegar mix if needed (still making sure to leave 1/2 inch of head space.)
Close the jars with new lids.
Once the water in the large pot is boiling, use the jar grabber to transfer the jars into the pot. Boil the jars for 20 minutes. Remove the jars using the jar grabber, and allow them to cool, undisturbed for at least 12 hours. Store in your pantry, then in the fridge once opened. Once opened, they will last in the fridge for a couple months.