How to recover corrupted chunks in a Minecraft world

Corrupted chunks show up as crashes when players enter an area, chunks that never load, or errors in the console about reading a chunk. You can fix them by restoring a snapshot, by replacing just the damaged region file from a backup, or by deleting that region so it regenerates.

Signs of a corrupted chunk

The server crashes or freezes whenever someone goes to a certain place.
A crash report says Ticking entity or Ticking block entity with the same coordinates every time.
The console shows errors like Failed to read chunk, Couldn't load chunk, or Chunk file at ... is in the wrong location.
An area shows as void or missing blocks.

Write down the coordinates from the crash report or error. They tell you which file to fix.

First: take a copy of the current state

Before changing anything, stop the server and take a snapshot, so you can go back if a fix makes things worse. Each server has 3 snapshot slots by default. If you need the slot for an older good snapshot, download the world folder instead.

Option 1: restore a snapshot

If you have a snapshot from before the corruption, restoring it is the simplest fix. It rolls the whole server back, including all worlds, plugin data and player inventories, to that moment. Anything done since is lost.

Option 2: replace just the damaged region file

Minecraft stores the world in region files, each covering 512 by 512 blocks. To find the one containing a block coordinate:

region X = floor(block X / 512)
region Z = floor(block Z / 512)
file     = r.<region X>.<region Z>.mca

For example, block -700, 1300 is in region -2, 2, so the file is r.-2.2.mca.

Where the files are:

World	Folder on Paper
Overworld	`world/region/`
Nether	`world_nether/DIM-1/region/`
The End	`world_the_end/DIM1/region/`

On Vanilla and Forge, the Nether and End are inside the main world folder: world/DIM-1/region/ and world/DIM1/region/.

Newer versions also have entities and poi folders next to region, with files named the same way. Entity data that crashes the server lives in entities.

If you have an older copy of the world (for example a downloaded backup):

Stop the server.
In the file manager, rename the damaged file, for example r.-2.2.mca to r.-2.2.mca.bad.
Upload the same file from your older copy into the same folder.
Start the server and visit the area.

Only that 512 by 512 area goes back in time; the rest of the world stays as it is.

Option 3: delete the region to regenerate it

If you have no backup and the area is not important, rename or delete the damaged file. The server generates fresh terrain there from the world seed. Any builds in that 512 by 512 area are lost. If the problem was a broken entity, try renaming only the matching file in entities first, which removes the mobs and items in that region but keeps the blocks.

Option 4: delete only the broken chunks

A region file holds 1,024 chunks, so deleting a whole region can remove more than you want. A desktop tool such as MCA Selector, used on a downloaded copy of the world, lets you select and delete individual chunks instead. Upload the edited region file back with the server stopped. The deleted chunks regenerate from the seed; everything else in the region is kept.

Preventing corruption

Stop the server properly instead of killing it, so it can save.
Keep disk space free. A full disk while saving is a common cause of corruption.
Turn on automatic daily snapshots (5 credits per day) or take snapshots before big changes.
Remove mods carefully, since removing a content mod can leave broken data behind.