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 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 SHA* backends are used, but even with the default backend it will work pretty well, as long as fsck preserved the modification time of the files.