On a vanilla server a world consists of three so-called dimensions. These dimensions are the overworld, the Nether and The End.
The main world is saved in the base path of the world folder. The End is saved in the DIM1 folder in your world directory and the Nether is saved the DIM-1 folder of your world directory.
Unfortunately all Bukkit based server softwares (Bukkit, Spigot, PaperMC) use a bit different world format. As soon as you start a vanilla server with a Bukkit based software the "DIM1" and "DIM-1" folder are moved into separate folders for each Dimension: world_the_end and world_nether.
If you want to convert your world back to the vanilla format you need to move world_the_end and world_nether back to their original place.
At Aternos this is done automatically for you as soon as you switch the server software. But if you want to download your world and play it in singleplayer you have to do this manually:
- Download all worlds on the worlds page.
- Unzip all the worlds
- Switch into the main world folder and check if there are already the DIM1 and DIM-1 folders and delete them if so
- Move world_the_end/DIM1 and world_nether/DIM-1 into your main world directory
After that you have a vanilla compatible world which contains the Nether and The End which can be moved to the saves folder of your local minecraft installation.
Please note that this only works if your current server software is a bukkit based one.