In Cell's original timeline, an alternate Future Trunks went into the past and helped Goku just as in the main timeline. Future Trunks and the Z Fighters manage to defeat the Androids and he travels back to his alternate future timeline. Since this was a completely different timeline, the events of Cell never occurred and he did not expect to encounter Cell (and may not have even been aware of Cell's existence). When he returned to Age 788 of his alternate future timeline, he disabled the other
Dragon Ball: 15 Things You Didn't Know About Trunks
Z Fighters, Animated Character Database
Future Bulma Briefs, Animated Character Database
Future Vegeta(Timeline 3), Animated Character Database
Trunks, Dragon Universe Wiki
The Daizenshuu's explanation of the Cell timelines SUCKS
Category:Saiyan, Animated Character Database
Category:Starseeds, Animated Character Database
Category:Killed In Action, Animated Character Database
The timelines in the Cell/Android sagas : r/dbz
How was the timeline where Cell kills Trunks created? - Page 2
How was Trunks born in both timelines? - Quora
Future Trunks Briefs, Animated Character Database
House of Vegeta, Animated Character Database
Timeline Explanation Chart : r/dbz