Spread a kitchen towel on the counter. Remove the warm jars from canner using the jar lifter. Drain the water back into the canner and line up the jars on the towel.
Using tongs, fill the jars with the onions. Add two sprigs of thyme to each jar.
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 of the jars with a clean damp towel to remove any residue.
Use the magnetic lid lifter to lift lids out of the warm water, center lid on the jar, and screw on band until it is fingertip tight.
Use the jar lifter to place the jars back into water bath canner leaving space in between them. Once jars are all in canner, adjust the water level so it is 1-inch over the tops of the jars. If adding water, use the hot water from your small pot.
Cover the canning pot and bring it to a rolling boil over medium-high heat. Once the pot boils, process half-pints for 10 minutes at attitude of 1,000 feet or less. (Adjustments must be made for altitudes greater than 1,000 ft. - see note)
When processing time is complete, turn off the heat and let the canner to cool for 5-minutes.
Spread a kitchen towel on the counter. Use a jar lifter to lift jars carefully from canner and place on the towel. Allow the jars to cool in place for 12 hours. You should hear the satisfactory "ping" of the jar lids sealing as the jars cool.
After 12 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 failed to seal, refrigerate the jar.
Remove the screw on bands and rinse the jars. Label, date, and store in a cool, dark location. Let the pickles 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.