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+I'm on an nfs mounted filesystem (some netapp somewhere).  This is repeatable, every time.
+
+    git init repo; cd repo;
+    git annex init repo
+    truncate -s 20M big
+    git annex add big
+    git commit -m "annexed file"
+    cd ..
+    git clone repo repo_copy
+    cd repo_copy;
+    git annex get .
+    git annex whereis big
+
+    #whereis big (2 copies) 
+    #   	9310b242-6021-4621-8cef-4548a00907ff -- here
+    #   	b3526e4d-38d7-4781-a9c3-436007899f1b -- origin (repo)
+    #ok
+
+    git annex drop big
+
+    #git-annex: /nfspath/repo_copy/.git/annex/objects/fM/4k/SHA1-s20971520--9674344c90c2f0646f0b78026e127c9b86e3ad77: removeDirectory: unsatisified constraints (Directory not empty)
+    #failed
+    #git-annex: drop: 1 failed
+
+    git annex drop big  # no error second time, I suspect nfs has caught up by now.
+    git annex fsck      # Doesn't know that the second drop succeeded.
+
+    #fsck big (fixing location log) 
+    #  ** Based on the location log, big
+    #  ** was expected to be present, but its content is missing.
+    #failed
+    #git-annex: fsck: 1 failed
+
+    git annex fsck
+
+    #fsck big ok
+
+    git annex whereis big
+
+    #whereis big (1 copy) 
+    #  	b3526e4d-38d7-4781-a9c3-436007899f1b -- origin (repo)
+    #ok
+
+I suspect git-annex is just too fast and optimistic for big slow nfs directories.
+