For some reason Gerudos didnt pay attention to the Timeline as they appear in OoT, MM disapear in TP and come back in FSA, were they in a region out of sight of the area Link searched? Or did they just go into hiding somewere?
I've thought about this myself. It's possible that the Death Sword was employed as an executioner by Ganondorf with the sole purpose of exterminating the entire Gerudo race. The remnants of the people went into hiding which explains why there are no Gerudo in Twilight Princess. The civilization reared itself again following Ganondorf's demise.
Well in TP, if I'm not mistaken (haven't played in a couple years), the Sages mention that Ganondorf was Gerudo and Demon Thief. As for the others.......dunno. Maybe Ganondorf killed them off or something.
EDIT: Wow, ALIT posts right before me
But yeah I think he and I are on the right track. It would make a lot more sense instead of the idea that they moved living location or "just weren't important"
I'm sure Hyrule is bigger than the Game world you play in. Gerudo Desert itself may have been much bigger than the part of it you got to go to and therefore there would be plenty of room for the Gerudo to be in hiding.