«The world» is not one folder, and knowing which is which is what stops a nether reset from taking the overworld with it.
The folders and what is inside
| Folder | What it holds |
|---|---|
world | The overworld: terrain, builds, and — importantly — player data and the level seed. |
world_nether | The Nether, in its own folder on Paper and Spigot. Vanilla keeps it inside world instead. |
world_the_end | The End, same arrangement as the Nether. |
world/playerdata | Every player's inventory, position and stats, one file per UUID. |
world/level.dat | The world's own settings: seed, spawn point, game rules, world border. |
world/region | The terrain itself, in .mca files of 32×32 chunks each. This is what gets big. |
Why the folder names matter
Server software decides how the dimensions are laid out. Paper and Spigot split them into three sibling folders; vanilla nests them inside the overworld folder as DIM-1 and DIM1. Moving a world between them is the usual reason a nether «disappears» after a migration.
Copy all three, always
When you download, migrate or back up a world, take world, world_nether and world_the_end together. They are one world in three boxes, and a world missing its Nether looks fine until someone builds a portal.
playerdata is inside the overworld folderRestoring only world_nether is harmless. Restoring only world rolls back everyone's inventory too, because that is where player files live.