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If you need to work with chunks, WorldEdit has you covered.
If you need information about the current chunk that you are standing inside, use this command.
Chunk: 8, -17 8/1b/c.8-h.dat
You can have WorldEdit list the chunks that your selection covers. Unfortunately, this command only prints to chat and so it has limited usefulness.
WorldEdit can generate a script to delete the chunks that a selection covers. WorldEdit will not delete the chunk by itself. You will have to run the script later to have the chunks actually delete. Before you can use this command, you must configure the shell script save type. The file will be saved to the root directory of the server (or rather, your working directory) as worldedit-delchunks.ext.
- IMPORTANT *
As far as I can tell, the warnings about Minecraft 1.3 refer to BETA 1.3, when file formats changed from per-chunk to per-region, not the changes (if any) in release 1.3. If true, then this won't even work in 1.2.5, and this cannot be used to edit out unwanted chunks within a region. -- Keybounce (unable to create a discussion page, sorry)