Howdy,
OK, your barn sub-panel is connected and working properly? OK, that means it has a master circuit breaker at the main service panel. That means all the wires are correct. You want to add a 50amp dual pole breaker with a interlock. OK but, you only want to use 2 wires. OK, in theory it sounds good, but when you switch over the interlock, (shuts off main, turns on generator breaker), the 2 wires are feeding the main panel, and the neutral and ground are still attached to the main service panel ground bar, and somehow connected to the sub-panel and generator. I understand what you want to do. It would be like saying use 2 separate 50 amp breakers, one at location 3 and the other at location 18 for your dual pole breakers. It's just not done.
Because of the limited draw at the barn sub-panel, because you have conduit in the ground, get the interlock for your panel, get you dual pole 50 breaker, and run 4 wires properly. Your not gonna break the bank with adding those 2 wires to a 100ft run. move on