When you're using git-annex you can git rm a file just like you usually would with git. Just like with git, this removes the file from your work tree, but it does not remove the file's content from the git repository. If you check the file back out, or revert the removal, you can get it back.

Git-annex adds the ability to remove the content of a file from your local repository to save space. This is called "dropping" the file.

You can always drop files safely. Git-annex checks that some other repository still has the file before removing it.

$ git annex drop iso/debian.iso
drop iso/Debian_5.0.iso ok

Once dropped, the file will still appear in your work tree as a broken symlink. You can use git annex get to as usual to get this file back to your local repository.