Minecraft – End data folder location

A useful tool that I've run into out there is something called Minecraft Region Fixer that may be able to help you solve your issue.

Minecraft Region Fixer is a command line-based tool that scans the files of a Minecraft world save and checks the file structures to see if there are corrupted chunks, or if there are other issues with the world save as well.

In my past experience using this tool, I did notice it was scanning the level.dat files for corruption, and it seemed to have the ability to repair the corrupted file.

If you are not familiar with using a command line, it will be pretty easy if you read the author's documentation on his post. He does a good job of being clear and thorough, and hopefully you will be able to use it to solve your problem!

According to Notch, both Nether and The End portals spawn naturally as well. If you happen to "meet" one of these portals, it will automatically generate a single chunk in the corresponding world to be able to place the matching portal in that world.

I'm not entirely sure, even though it seems this way, that if you see one of the two, it does this for both. Notch has never released anything about this.