Flapper connection had two pins 180 degrees apart to catch the flapper arms. One broke. How can I repair

Get a new flapper with rubber ring. Remove the pin on the other side. The new flapper (at least some brands) will come with a rubber ring to slip down the overflow pipe.

And if Harold's fix doesn't work, you need to replace the tube.

And if Harold's fix doesn't work you have to replace the entire FLUSH VALVE ASSEMBLY (not just the tube)... ;)

See image

Mark

Another option.