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Alright, so I just built a nether portal into my world and popped over into the nether just long enough for it to generate the world (on account of not having the supplies to actually go on a nether expedition quite yet), but when I returned through the portal, I appeared not back where I first left from, but instead in my old superflat texture-test world which had been deleted. This was easy enough to fix, as I had TooManyItems installed so I just saved my invantory and committed suicide, waking up back in my bed in the original world, but it still doesn't answer the question of why this happened and how to prevent it.

So... why did this happen and how do I prevent it?

Alright Update: after some testing I have determined that this error has been happening consistently every single time I try to leave the Nether, despite having destroyed the nether portal in the "deleted" world, because new ones just keep popping up.

1) A nether portal doesn't necessarily provide a round trip. You can come back far away from where you went in.

2) If you delete a world and then create a new world with the exact same name, the chunk files are stored in the same directory. If any part of the old world didn't get completely deleted from the disk, then you can run into chunks from the old world.

I think this combination explains what is happening to you.

What? Ok, that is the weirdest thing I've ever heard. Try these steps:
1. BEFORE you go into the nether on your original world, press F3. Take down the X, Y and Z Co-ordinates.
2. Travel to the nether.
3. Leave the nether
4. When you return in your Superflat world, look at the co-ordinates, and travel to the co-ordinates you wrote down earlier.
5. If you wind up in your original world, than what Gerbil said has been confirmed. If you do not, I don't know what to tell you.

Quote from Waspus500

What? Ok, that is the weirdest thing I've ever heard. Try these steps:
1. BEFORE you go into the nether on your original world, press F3. Take down the X, Y and Z Co-ordinates.
2. Travel to the nether.
3. Leave the nether
4. When you return in your Superflat world, look at the co-ordinates, and travel to the co-ordinates you wrote down earlier.
5. If you wind up in your original world, than what Gerbil said has been confirmed. If you do not, I don't know what to tell you.

That worked. I'm not sure how or why, but that worked.

So now what?

Then it is just a chunk error, with the chunks loading from the wrong directory. There's nothing you can do, unfortunately.

EDIT: You could try deleting the superflat world out of your .minecraft/saves folder.

Quote from Waspus500

Then it is just a chunk error, with the chunks loading from the wrong directory. There's nothing you can do, unfortunately.

EDIT: You could try deleting the superflat world out of your .minecraft/saves folder.

Um... bit of a problem with that. There were two saves called "New World". I deleted one of them, and started the game to find the correct world disappeared from the "Select World" menu. I figured that must be the correct one, so I exited the game and restored it and deleted the other one. I opened the game again, and the correct world hadn't reappeared. I exited the game and restored both saves, but the correct world still hasn't reappeared. What's going on here?

Try restoring only the correct one.

Quote from Waspus500

Try restoring only the correct one.

Still not working.

Weird. You still have the folder, right? If so, maybe delete the session.lock?

Quote from Waspus500

Weird. You still have the folder, right? If so, maybe delete the session.lock?

Yeah, I've still got the folder.

What's the session.lock do?

The session.lock saves the data about the last session, so you can quickly open the map again (Chunks loaded, etc.) Try deleting that.

no no no.. the data was never loading from two directories...
FIxing this required carefully deleting individual chunk files, or maybe even using McEdit.
Not deleting whole saves....

Quote from Waspus500

The session.lock saves the data about the last session, so you can quickly open the map again (Chunks loaded, etc.) Try deleting that.

Nope. Still hasn't reappeared

Try loading the world in MCEdit. Simply open MCEdit, click "Open World", and navigate to where you saved the file. If it opens, then good. Post whether it opens in MCEdit or not.

EDIT: Try renaming the folder itself, the correct world, and put it back into the saves folder, along with doing the MCEdit thing.

Quote from Waspus500

Try loading the world in MCEdit. Simply open MCEdit, click "Open World", and navigate to where you saved the file. If it opens, then good. Post whether it opens in MCEdit or not.

EDIT: Try renaming the folder itself, the correct world, and put it back into the saves folder, along with doing the MCEdit thing.

Okay... this is really weird. I've opened all of my saved worlds in MCedit, and none of them is my current world. None of them is the deleted world either. They're all old worlds that I haven't deleted. I'm so confused.

When you say "None of them is the current world," you mean none of the worlds are the world you are trying to restore? Or all of the worlds are different? Please clarify.

Quote from Waspus500

When you say "None of them is the current world," you mean none of the worlds are the world you are trying to restore? Or all of the worlds are different? Please clarify.

Yes, that's exactly what I mean. Even though I put back both of the saves that I deleted.

Is the folder that you are putting back empty? Cause it sounds like it is...

Quote from Waspus500

Is the folder that you are putting back empty? Cause it sounds like it is...

No, its not empty. Everything that was in it is still in it. It just isn't the world that I'm trying to recover. Neither is the other folder. Every folder is some previous world of mine that I'd never deleted. Logically this should mean that my current world is in some other additional save file, which is now missing, but that doesn't add up because I only deleted two save files, and I've since put both of them back. And yet there's still one less world than there was before. Fourteen minus two plus two should equal fourteen, but somehow fifteen minus two plus two is equaling fourteen, or something equally absurd.

God, its like discovering my copy of Minecraft is a quarter of an inch larger on the inside than it is on the outside.