Lay a dry kitchen towel on the counter. Use the jar lifter to remove a jar from the canner. Drain the water back into the canner, and place on the towel. Keep the remaining jars in the canner so they stay hot.
Using tongs, fill the jar with the onions, add two sprigs of thyme, then ladle hot pickling liquid over the onions leaving a 1/4-inch headspace.
Run the bubble popper through the jars to release air bubbles. Wipe the rim to remove any residue, center a lid on the jar, and screw on a band until it is fingertip tight. Use the jar lifter to place the jar back into the canner, and repeat with the remaining jars.
Once all the jars are in canner, adjust the water level so it is two inches above the jar tops.
Cover the canner and bring to boil over high heat. Once water boils vigorously, continue boiling for 10 minutes at altitudes of less than 1,000 feet. Adjust processing time for your altitude if necessary (See Notes).
When processing time is complete, turn off the heat, and let the canner cool down and settle for about 5 minutes.
Spread a dry kitchen towel on the counter. Remove the cover by tilting lid away from you so that steam does not burn your face.
Use the jar lifter to remove the jars from canner and place on the towel. Keep the jars upright, and don't tighten bands or check the seals yet. Let sit undisturbed for 12 to 24-hours to cool.
After 12 to 24-hours, check to be sure jar lids have sealed by pushing on the center of the lid. The lid should not pop up. If the lid flexes up and down, it did not seal. Refrigerate jar and use up within a week.
Remove the screw on bands and wash the jars. Label, date, and store in a cool, dark place for 12 to 18 months. Let the pickled onions stand for about a week before opening for the flavors to develop.
Use home canned jars within 12-18 months. Makes about 6 half-pint jars of picked red onions. Refrigerate the jar after opening.