These problems were dealt with in a few ways. One supposably Saturngirl made it so he didn't recall the adventures when SB returned to his present. In the last Legion post I did,a foe torments Superboy be showing him that his parents will die despite anything he does. This leads to him deciding to never return to the future again and Saturngirl puts the full whammy on him so he will never return. This story was about how all that breaks down ans he creates this other persona "Reflecto" to live out his life in the future (Didn't superman do the same when he adopted the Gangbuster persona ?).
Problems with these ideas of what Superman recalled about the future were numerous. In Action comics 500 at the opening of the Superman museum, there is a Legion display and Superman talks about his experiences with them and then..he just never saw them again.
Actually I kinda like Geoff Johns idea that there was no superboy except in the Future. The Legion picks up Clark takes him to the future he does all his Legion stuff and then returns to the 20th century minutes after he left. Dunno, I think it will always be a wonky problem.