[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2016-09-05T18:14:24Z"
 content="""
I do not reproduce this bug with the current version of git-annex.

Using a directory special remote:

	joey@darkstar:~/tmp/me>git annex copy foo --to d
	copy foo (to d...) 
	ok                      
	joey@darkstar:~/tmp/me>sudo rm ../d/e70/8a4/SHA256E-s30--8f6ec07ba3543f8ae5da1d85602a389e36b15f291c2d1e02bc1920565c1a1f25/SHA256E-s30--8f6ec07ba3543f8ae5da1d85602a389e36b15f291c2d1e02bc1920565c1a1f25
	fsck foo (fixing location log) 
	  ** Based on the location log, foo
	  ** was expected to be present, but its content is missing.
	failed
	(recording state in git...)
	git-annex: fsck: 1 failed
	joey@darkstar:~/tmp/me>git annex whereis
	whereis foo (1 copy) 
	  	e32ee842-ff63-4c23-b239-53cd887d79b1 -- joey@darkstar:~/tmp/me [here]
	ok

But, you omitted the "error message from special remote" for some reason.
That information you omitted is almost certianly *crucial* information to understanding
your bug report. 

If git-annex thinks it was not able to talk to the special remote at all,
it won't record it as not having the file, because more likely the special
remote is temporarily not accessible.

At the moment, I see no indication of a bug. I'll leave this open for a little while marked moreinfo.

(I'm also curious how you managed to report this bug without giving any
title at all. I had to rename ".mdwn" to a more reasonable filename.)
"""]]