Chunk Pregen has a feature to delete chunks live from the running server (if they are unloaded) from the disk. As long you know where its coordinate where it is.
This is the mod that can do it: https://minecraft.curseforge.com/projects/chunkpregenerator
(server only needed)
Documentation:
/pregen delete deleteChunk
Description: Deletes a Single Unloaded Chunk
Parameters:
X Position: The X Chunk Position of the Deletion. (if ‘b’ infront of the number or after ~ means block position)
Z Position: The Z Chunk Position of the Deletion. (if ‘b’ infront of the number or after ~ means block position)
(Optional) Dimension: The Dimension the Deletion should be happening in
(Optional) Delay: How long the Deleter should wait until it should start (in ticks)
Examples:
deleteChunk
/pregen delete deleteChunk 100 200
- Deletes a Unloaded Chunk at X100 Z200 at the Dimension that the sender is at
/pregen delete deleteChunk b100 b200 -1 200
- Deletes a Unloaded Chunk at X6 Z12 in the nether and waits 10 seconds until starting it
As long the chunk is not loaded it can delete it. (it wont load the chunk it just tries to delete the data at the position.