6 month old site is suddenly throwing 404s
Since files that begin with a dot are hidden by default in Unix-based systems like OS X, Craft ships with a “htaccess” file rather than “.htaccess”. If you are using Apache and want to use this file, you need to rename it to .htaccess when you upload it to your web server.

Not sure why suddenly your site stopped working, but I can tell you that Craft auto-updates will only ever touch files within the craft/app/ folder, so if your .htaccess file was misnamed, it’s definitely not due to a Craft auto-update.