If you use the Pre-Installation and Setup Wizards all files are backed up for all website folders at the same time. On the AutoRestore page the AutoRestore/Quarantine Controls & Backup Status are now manual controls that you would use in these types of scenarios.
You have downloaded your Theme’s functions.php file from your website and edited it and added some new code in that file and uploaded it back to your website.
You manually uploaded some new files to your website.
http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/
AutoRestore/Quarantine Correct Usage
AutoRestore/Quarantine (ARQ Infinity) IDPS is a real time file monitor that monitors all of your website files for any changes. When manually uploading files with FTP or modifying files on your website follow these simple procedural steps for AutoRestore/Quarantine (ARQ) to avoid having those files autorestored and / or quarantined. If files are sent to Quarantine then use the Restore File option in Quarantine to restore those files.
1. Turn ARQ Off.
2. Upload or modify files on your website.
3. Click the appropriate Backup Files button: Root Files, wp-admin Files, wp-includes Files or wp-content Files Backup Files button.
4. Turn ARQ back On.
Regarding the “BPS Pro AutoRestore Automatic Shutdown & Backup Notice” message:
The BPS Pro AutoRestore Automatic Shutdown & Backup Notice does not display on Network/Multisite site types since the Network Administration panel is outside of the loop.
If you do not have a Network/Multisite site then how did you install the plugin update?