Comment 8 for bug 1194074

As a suggestion to all affected: I suggest that you do not use the default document root (/usr/share/nginx/www/) for your files, and instead use a different document root for your sites. By using the default document root, you are inviting issues such as these to occur.

I also suggest that you keep regular backups, which is part of server administration, to make sure that you don't lose your data.