But then Link returns to his childhood time. As a child, Link warns Zelda about Ganon, and preempts the future (where Ganon takes power and adult Link defeats him) from happening. So, there are at least two timelines.

Majora's Mask follows this child Link in one of the few explicit sequels in the series.

But then Wind Waker faces off against the Ganon defeated by adult Link. This is explicitly referenced in the text but it's not so clear-cut a sequel.

Meanwhile, Ocarina of Time was explicitly a prequel to A Link to the Past (depicting the events described in ALttP's backstory). But (1) some events don't quite line up and (2) the continuity of games established in the other timelines can't really neatly fit the ALttP-LA-OoS/OoA-LoZ-LA chronology. So a third timeline is just the neatest way to do it.

None of this really matters for playing or understanding the games, though. With the exception of Majora's Mask (and Phantom Hourglass / Spirit Tracks to a lesser extent), each Zelda game can be enjoyed as someones first Zelda.