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 $ sudo chown you:you recovered-content $ chmod -R u+w recovered-content $ git annex add recovered-content $ git reset HEAD recovered-content $ rm -rf recovered-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. So, this works as long as you're using one of the SHA* or other checksumming backends, which is the default.