Alright, so my world data might be useless after all.
After shutting down the server to upload my world and restarting the server, my world data got reverted to a very old state and I can't reproduce the bug the way I did before.
So, the data provided is actually an old version of my world.
I will then provide all I did with more details:
All computers are under Win7 x64
I started from a new install of Minecraft 1.8.4 (nothing modified except player skins)
I created a world in single player
I built some stuff in that world
I installed a Minecraft 1.8.4 server in a folder on my desktop folder (the desktop folder does strange things on Windows sometimes, could it be related?)
I made a copy of the single player world folder to the server folder and renamed it "world"
I started the server (after modifying the eula file)
I installed Minecraft 1.8.4 on a laptop in the same LAN as the server, connected through wireless.
I increased the allocated memory on the laptop to 3 GB since I had some issues when I tried to play shortly in single player (e.g. long delay for the world to update after destroying a block).
I connected from the laptop to the server (using Direct Connect, the game doesn't show in the LAN server list)
I also had some issues to connect (errors about invalid session): I deleted the session lock file and restarted all to make it work
I played a few days in a row from the laptop without restarting the server (there was always a single player on the server at any time)
After some time, I dug a very long tunnel (a few chunks long).
After going back to my house then going again to the tunnel, I noticed the end farthest from my house was closed. I dug it again and noticed that the blocks would come back every time I would go back and forth between it and my house. I assume all changes to that chunk were reverted every time they were unloaded.
I submitted my first comment here, then stopped the server to upload the world data.
After restarting the server, everything in my world was reverted to its state when I first copied the (originally single player) world to the server folder (losing everything that was done in multiplayer, but not previous changes)
I modified the chunk that was previously reverting and my house, I stopped and restarted the server: this time all changes were kept.
The server GUI never displayed any message in the log/chat window.
So, to sum up with some interpretation:
It seems my world was only changed in the memory and never saved on disk during all the first session of the server
Changes stopped being saved even in memory at some point, even though they would still show as long as the chunk was loaded
after restarting the server, the data is back to what it originally was but now changes are saved between server sessions (at least during the few short tests I did, the bug might come back)
Here's my world: http://www.mediafire.com/download/aioa4fxuhyxotdm/world.7z
I will provide the coordinates where it happens later (I'm in a rush at the moment, sorry).
This seems to affect my world too:
Minecraft Server 1.8.4 under Win7, client on LAN under Win7
Steps:
I created a world in single player (btw, the 4 worlds I created with 1.8.4 all start in a Taiga biome, weird?) and played a few hours in it
I copied the world to the server folder to play it in multiplayer
I connected from another computer (and I was the only player on the server all the time)
at one point, I dug a very long tunnel through a mountain
If I go back and forth all the way through the tunnel, the chunk at one end of the tunnel will consistently be regenerated from the world seed, discarding all my previous changes to the chunk.
EDIT: World data available to download, see this comment: https://bugs.mojang.com/browse/MC-2548?focusedCommentId=225913&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-225913
I followed the steps that I mentioned above again (except using a single computer and without re-installing clean copies of Minecraft and Minecraft server) without reproducing the bug...
This time, I had no session lock error and the generated world didn't start in a taiga biome (for once).