Combine cucumbers, onions, and salt together in a colander fitted over a bowl; place in the refrigerator for cucumbers and onions to drain, 8 hours to overnight.

Mix vinegar, sugar, water, flour, turmeric, ginger, and black pepper in a large saucepan; bring to a boil. Cook, stirring occasionally, until mixture is thickened, about 5 minutes. Add cucumbers and onions; boil for about 10 more minutes.

Sterilize jars and lids in boiling water for at least 5 minutes. Pack the relish into the hot, sterilized jars, filling the jars to within 1/4 inch of the top. Run a knife or a thin spatula around the insides of the jars after they have been filled to remove any air bubbles. Wipe the rims of the jars with a moist paper towel to remove any food residue. Top with lids and screw on rings.

Place a rack in the bottom of a large stockpot and fill halfway with water. Bring to a boil and lower jars into the boiling water using a holder. Leave a 2-inch space between the jars. Pour in more boiling water if necessary to bring the water level to at least 1 inch above the tops of the jars. Bring the water to a rolling boil, cover the pot, and process for about 15 minutes.

Remove the jars from the stockpot and place onto a cloth-covered or wood surface, several inches apart, until cool. Once cool, press the top of each lid with a finger, ensuring that the seal is tight (lid does not move up or down at all). Store in a cool, dark area.