Aonuma said all locations in Twilight Princess (Ordona, ect..) are locations from Ocarina of Time. Everything in Ocarina of Time appears in Twilight Princess, he said. It's the same world centuries or so alter.
Therefore, Twilight Princess locations (Ordona, Lake Hylia, Kakariko) are all locations from Ocarina of Time - CENTURIES LATER.
And I'm not saying the Kokiri died- they left Kokiri Forest and went into Faron right near it, and the Forest Temple became was where they left and says something: they moved.
And understand the difference in graphics and time- Twilight Princess has all locations from Ocarina of Time and shows them over a century later - on a much more powerful graphical engine. Therefore, everything in Ocarina of Time appears in Twilight Princess. The locations.
We have abandoned Kokiri Forest, showing they moved to the Forest Temple (which amy or may not be the same one from Ocarina of Time, overgrown by forest life) and there you have their synbols and ruins outside the temple, and that's abandoned, too... Go to Castle Town... you have Princess Agitha, a childish blonde, nature-looking girl with no parents. Her house is composed of nature and has a tree in the centre.
At the end of Ocarina of Time (credits), the Kokiri were shown to be leaving the forest, and the forest was seen empty. They were with the people of Castle Town. Over a century later, we see an apparant Kokiri girl in the Castle Town.
...You don't quite get the picture. The Zoras did move, but they didn't move Zora's Fountain - they built over it. Their throne room in Twilight Princess is the fountain, built over the fountain. The enterence to the domain in Twilight Princess has a huge waterfall, and so does Zora's Fountain, so they moved over to it and built over it. Because they abandoned the former Zora's Domain and moved slightly north over to build over the fountain, the rivers obviously changed shape and course.