Suppose something goes wrong, and fsck puts all the files in lost+found. It's actually very easy to recover from this disaster. First, check out the git repository again. Then, in the new checkout: mkdir recovered-content sudo mv ../lost+found/* recovered-content git annex add recovered-content git rm recovered-content git commit -m "recovered some content" git annex fsck The way that works is that when git-annex adds the same content that was in the repository before, all the old links to that content start working again. This works particularly well if the SHA1 backend is used, but even with the default backend it will work pretty well, as long as fsck preserved the modification time of the files.