Working quickly, divide the chiles, garlic, thyme, red pepper flakes, and peppercorns among the jars. Using tongs or a slotted spoon, transfer the hot carrots to the jars (do not pack them too tightly) and fill in empty spaces loosely with slivers of onion. Ladle the hot pickling liquid into the jars, leaving 1/2-inch headspace at the top. Use a chopstick to remove air bubbles around the inside of each jar. Use a damp paper towel to wipe the rims of the jars then put a flat lid and ring on each jar, adjusting the ring so that it’s just finger-tight. Return the jars to the water in the canning pot, making sure the water covers the jars by at least 1 inch. Bring to a boil, and boil for 15 minutes to process.
Remove the jars to a folded towel and do not disturb for 12 hours. After 1 hour, check that the lids have sealed by pressing down on the center of each; if it can be pushed down, it hasn’t sealed, and the jar should be refrigerated immediately. Label the sealed jars and store.