In reply to Dimitris Abrazis.

@Dimitris - Then run your site through a source control system (git, mecurial or subversion). Automatic background updates are disabled if they detect you're running from source control. Once you know of an update, apply it and test it on your dev or test environment. Once everything looks good, commit your new changes to source control and push it out to the live server. The extra benefit of source control is that you can roll back the entire site if needed or just roll back a particular file. And the benefit of having a history of site changes to compare against when troubleshooting issues.