Um... no. Uh. It would make the crappiest and most redundant, pointless plot if the works of FS were undone within a few years. It makes the ending useless and the game itself, pointless if "oh look it didnt' matter anyway".
But it didn't. It didn't effect th storyline whatsoever. No new consequences were created, things went back to how they were. It was just a minigame that opened a door for FSA. Thusly, Sequel-age.
As for all this map bullshit, lighten up you guys. Are you that ornery? There's a difference between the Triforce and a map. Not even the developers are that much concerned about the timeline, and the only way to make the geography consistent would be to COMPROMISE THE GAMES, which is NOT an option for their business. People will get pissed about playing in an identical/similar enviornment all the time and Zelda won't be fun anymore. Half the fun of Zelda is discovering and exploring new areas. "And lesse, the Lost Woods? *yawn.* cool. Here's the stump Saria sings that song. Eh. The boss is probably where the Deku Tree is."
As for the reasons they don't have a drop-list and put in all these "realistic features" is obvious. EYE CANDY! that's the reason we have any graphics that are SNES-quality or higher, or we'd be playing TWW in 8 bit. (which would probably be kinda cool, but I digress)
Get the hell OVER it. The Geography is not a tool you can use to warp your theories to fit your wants and needs. It's a peice of eye candy you can use to clear up consistencies that don't contradict the timeline, like the Death Mountain in OOT and TWW. Get over yourselves. You don't know the intentions of the creators, you don't know what they are planning, and you especially don't know the significance of the geography, if you can't even accept Fyxe's reasoning. But I guess that's what we get for arguing with british dudes.