Permanently damaged chunks, ghost chunks

After a server crash several .mca files got damaged, I'm not sure if the damage is from an incomplete save or file system error, they are simply damaged.

Note that this .mca file is 100% broken by vanilla server, no 3rd party tools has touched it.

When the server is running again with the .mca most chunks are ok, a few are not. These bad chunks cause a lot of error message on the console such as this one:

Chunk file at 10,-139 is in the wrong location; relocating. (Expected 10, -139, got 8, -144)
Chunk file at 11,-142 is in the wrong location; relocating. (Expected 11, -142, got 3, -139)
Chunk file at 11,-138 is in the wrong location; relocating. (Expected 11, -138, got 6, -139)
Chunk file at 14,-136 is in the wrong location; relocating. (Expected 14, -136, got 15, -136)
Chunk file at 15,-137 is in the wrong location; relocating. (Expected 15, -137, got 7, -156)
Chunk file at 16,-137 is in the wrong location; relocating. (Expected 16, -137, got 20, -151)

java.lang.Exception: Stack trace
at java.lang.Thread.dumpStack(Thread.java:1342)
at abd.a(SourceFile:504)
at abq.a(SourceFile:274)
at abq.a(SourceFile:72)
at abq.a(SourceFile:60)
at iw.f(SourceFile:125)
at iw.c(SourceFile:76)
at iv.<init>(SourceFile:26)
at iu.a(SourceFile:172)
at iu.a(SourceFile:203)
at gs.a(SourceFile:121)
at gs.c(SourceFile:164)
at gs.a(SourceFile:98)
at jd.d(SourceFile:164)
at jd.c(SourceFile:56)
at id.a(SourceFile:49)
at ic.b(SourceFile:29)
at net.minecraft.server.MinecraftServer.r(SourceFile:478)
at hx.r(SourceFile:248)
at net.minecraft.server.MinecraftServer.q(SourceFile:395)
at net.minecraft.server.MinecraftServer.run(SourceFile:329
)
at gn.run(SourceFile:565)

followed by an infinite stream of these:

Wrong location! pz['Sheep'/18580, l='world', x=188.89, y=65.00, z=-2262.58]
java.lang.Exception: Stack trace
at java.lang.Thread.dumpStack(Thread.java:1342)
at abd.a(SourceFile:504)
at zh.a(SourceFile:1343)
at ix.a(SourceFile:491)
at zh.g(SourceFile:1297)
at zh.h(SourceFile:1204)
at ix.h(SourceFile:385)
at net.minecraft.server.MinecraftServer.r(SourceFile:460)
at hx.r(SourceFile:248)
at net.minecraft.server.MinecraftServer.q(SourceFile:395)
at net.minecraft.server.MinecraftServer.run(SourceFile:329)
at gn.run(SourceFile:565)

Expected behavior:
Once a broken chunk is detected it should be removed and regenerated, possible save a backup in another file.

Our only solution to this crash was to restore from backup.