So this has happened several times now. After having a multiplayer server up for several hours I shut it down with no one logged on. No errors, no crash. When I start it up and log back in, several random chunks have rolled back to earlier states (but not back to world creation). Player inventory seems unaffected. Running: [22:01:31 INFO]: This server is running CraftBukkit version git-Spigot-2ec6f06-7722428 (MC: 1.8.3) (Implementing API version 1.8.3-R0.1-SNAPSHOT) On the plus side it has given us an unlimited supply of iron as the forges were full in one of the chunk it keeps reverting back too. more info: settings: allow-end: true warn-on-overload: true permissions-file: permissions.yml update-folder: update ping-packet-limit: 100 use-exact-login-location: false plugin-profiling: false connection-throttle: 4000 query-plugins: true deprecated-verbose: default shutdown-message: Server closed spawn-limits: monsters: 70 animals: 15 water-animals: 5 ambient: 15 chunk-gc: period-in-ticks: 600 load-threshold: 0 ticks-per: animal-spawns: 400 monster-spawns: 1 autosave: 6000 aliases: now-in-commands.yml database: username: bukkit isolation: SERIALIZABLE driver: org.sqlite.JDBC password: walrus url: jdbc:sqlite:{DIR}{NAME}.db #Minecraft server properties #Sat May 09 21:31:40 EDT 2015 spawn-protection=16 generator-settings= force-gamemode=false allow-nether=true gamemode=0 enable-query=false player-idle-timeout=0 difficulty=2 spawn-monsters=true op-permission-level=4 resource-pack-hash= announce-player-achievements=true pvp=false snooper-enabled=true level-type=DEFAULT hardcore=false enable-command-block=false max-players=20 network-compression-threshold=256 max-world-size=29999984 server-port=25565 debug=false server-ip= spawn-npcs=true allow-flight=false level-name=world view-distance=10 resource-pack= spawn-animals=true white-list=false generate-structures=true online-mode=true max-build-height=256 level-seed=2495308415750545648 motd=A Minecraft Server enable-rcon=false
It may be a corrupted chunk and the server fails to save it because the data is messed up. If it is not that, it may be because you don't have enough storage on your server.
I was able to force a save of one of the chunks that kept reverting by issuing a server command from the command line "save-all". No errors and it saved my one quick change (dug a hole). I have it running on a separate 240 GB SSD with about 95 GB free.
Follow-up: The server is still not saving every 30 minutes like I would expect but the save-all command works if you manually use it. I'm ok with this work around. I'm still worried what will happen if I lose power or it crashes while I'm at work.