Those would be 2 different files. There are 2 totally different things that are checked – if an existing file is modified/tampered with or if a new file is uploaded to your website.
Hypothetical Examples:
You have an existing file named exampleA.php and a hacker has injected code into the exampleA.php file. AutoRestore will restore the exampleA.php file that is in AutoRestore backup and replace the exampleA.php file that has been tampered with. Before that tampered file is overwritten it is sent to Quarantine. The exampleA.php file will contain the hackers code. The exampleA.php file under your website files that was hacked has now been restored/replaced with a good file that is not hacked.
A hacker uploads a hacker file named exampleB.php to your website. There is no exampleB.php file in AutoRestore backup because this is a new hacker file that has been uploaded to your website. The exampleB.php file will be sent to Quarantine.