Dear all,
        I had (snif!) and indirect repo with 2.7 of pdf files with filenames were manually added by me with author and title, and took years of work. I had them in a git annex repo from quite some time.  
Now I'm trying to sync them to an usb drive. Main repo lives in an ubuntu box with ext4 filesystem. I failed many times to do this, both on fat and exfat external drives (direct).  
As I was failing, I tried to to a test on the same local filesystem. So I have my main repo in /home/juan/papers and the other in /tmp/papers.  
While trying to sync them using the assistant, i noticed that most of the folders and symlinks from the main repo just dissapeared. 
I still have them in .git/annex/objects but I don't know how to recover the links. 
I must say I'm an everyday git user, and big fan of git-annex but I'm trying to use it for six months without luck. I think I will quit after recovering the data, if possible.

EDIT 1
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After digging around a bit, I found that I had the keys, and could find out the original filename, for example:

    git log --stat -S 1279
    commit a6362df13d728037875320a457182acb073d08ea
    Author: Juan Cardelino <x@gmail.com>
    Date:   Fri Nov 21 11:25:31 2014 -0200

     2013_august/feature_matching_by_searching_maximum_clique_on_high_order_association.pdf | 1 +
     LevelSets/fedkiw/stanford2002-06.pdf                                                   | 1 +
     new/nfa/00106994.pdf                                                                   | 1 +
     3 files changed, 3 insertions(+)

How can I recover them?

EDIT 2
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Seems that I overwritten my repo with a new repo. Because git log only shows 4 entries from today. Is it possible that the webapp has made that?
