Make the syrup. In a large pot, combine sugar, canning salt, turmeric, mustard seed, red pepper flakes, garlic, and ginger. Pour in apple cider vinegar and stir well. Bring to a boil over medium heat, stirring until sugar dissolves. Reduce heat to low and simmer uncovered for 30 minutes, stirring occasionally.
Prepare jars. Wash jars, lids, and rings in hot soapy water. Place jars in a water bath canner, fully submerged. Bring to a simmer (180°F) and keep hot until ready to fill.
Add pineapple and jalapeños. Add chopped pineapple and sliced jalapeños to the simmering syrup. Return to a gentle boil and cook for 5 minutes, stirring occasionally.
Fill jars. Ladle hot pineapple mixture into hot jars using a canning funnel, leaving 1/2 inch headspace. Remove air bubbles with a chopstick or bubble remover. Adjust headspace if needed. Wipe rims with a clean, moist towel. Place lids and tighten rings to fingertip tight.
Process. Place jars in the water bath canner with at least 1 inch of water covering them. Bring to a rolling boil, covered. Process half-pint jars for 15 minutes (20 minutes for pint jars), adjusting for altitude.
Rest and check seals. Turn off heat, remove canner lid, and let jars sit for 5 minutes. Remove jars and place on a towel-lined surface. Do not disturb for 24 hours. Check seals — lids should not flex when pressed. Remove rings, clean jars, label, and store in a cool, dark place.