In a noninertial frame both the bodies will experience equal acceleration in the horizontal direction. So the experiment result will change in the accelerating car.
After applying pseudo forces the motion can be analyzed as if in an inertial frame. Since the sum of external forces are not zero now, hence the equations (i) "Velocity of separation = Velocity of approach" and (ii) "final momentum = initial momentum" do not remain valid in the accelerating car.