The one who appeared and killed Robo Frieza was from a different future in which the androids destroyed everything so the events of Super can never happen to him.
During the Cell Saga when Cell explains how he came from the future he states he already "disposed" of Trunks to steal the Time-Machine. I also recall him pointing out during the Cell Saga that altering the past won't change his own future or the future of the Z Warriors he was with, but will instead create an alternate timeline (I think it was after they found Dr. Gero's lab and Krillin suggested that Trunks go back in time further and destroy it before the Androids are activated)
To prove this, after Cell was discovered to be an "Android" created by Dr. Gero, Krillin and Future Trunks went back to his lab and destroyed the Laval Cell who was hidden there and it didn't cause the mature Cell they were currently fighting to disappear.
Also on the Wikia for Future Trunks
Future Trunks (未来のトランクス), referred to in the series simply as Trunks, is the Saiyan and human hybrid son of Vegeta and Bulma from an alternate future. By the time Present Trunks was born, the timeline had been altered by Future Trunks' and Cell's trips to the past. Therefore, the two Trunks had completely different lives (as opposed to those who lived before the Time Machines arrived, they lived exactly the same lives as their counterparts until the point at which the two timelines diverge: three years before the androids arrived).
Source: Dragonball Wikia - Future Trunks
So Future Trunks (the one that killed Robo Freeza) probably didn't go beyond Super Saiyan because Goku and Vegeta, who knew of the other levels, are dead and most of his time was spent fighting the Androids.
The Trunks seen in Super probably won't go back in time because there is no need to. And anyway, if the planet is destroyed Beerus will just restore it so he can keep getting desserts.