This theory states that some Zelda games take place in one time line, while other games take place in another. This theory has been thrown around by fans for years, but few people really took it seriously, partly because it didn't seem to be what the creators intended, and partly because it seems like an easy way out. However, recent statements by the creators have made fans have second thoughts. Miyamoto and Aonuma participated in a Wind Waker summit in 2002. The uncut version of the interview from Gamepro reads as follows:

Q: Where does The Wind Waker fit into the overall Zelda series timeline?

Aonuma: You can think of this game as taking place over a hundred years after Ocarina of Time. You can tell this from the opening story, and there are references to things from Ocarina located throughout the game as well.
Miyamoto: Well, wait, which point does the hundred years start from?
Aonuma: From the end.
Miyamoto: No, I mean, as a child or as a...
Aonuma: Oh, right, let me elaborate on that. Ocarina of Time basically has two endings of sorts; one has Link as a child and the other has him as an adult. This game, The Wind Waker, takes place a hundred years after the adult Link defeats Ganon at the end of Ocarina.
Miyamoto: This is pretty confusing for us, too. (laughs) So be careful.

This statement has led some people to believe that the creators now intend for Hyrule's history to be divided into parallel time lines. The time line split occurs in OoT, with one time line in the past and one in the future. Below I give one possible way this theory could work out.