I have a Minecraft server control script called rfwadmin ( https://github.com/Thue/rfwadmin ). That script uses the save-all command for saving. On minecraft_base.sh line 518 ( https://github.com/Thue/rfwadmin/blob/master/fsroot/var/lib/minecraft/minecraft_base.sh#L518 ), I send the /save-all command, and wait for the line "save complete" to appear in the log. Right after I see "save complete", I do a filesystem copy "cp -r" of the presumably saved files.

But the files are not always saved in the copied version!

One way to reproduce in vanilla is to fly over the terrain placing blocks, touching as many chunks as possible quickly. I think that the more chunks you touch, the higher chance that not everything is saved.

While I can sometimes reproduce the issue in vanilla, it is easier to reproduce using craftbukkit and worldedit. Do a "//replacenear 100 bedrock diamond", and you can be sure not all chunks are saved if you do a save-all+"cp -r" right afterwards.