FTP (server) and HTTP (server) are two completely different things and they don’t normally communicate with each other unless you create code that performs FTP tasks in PHP/HTTP level code, but they will still not be able to communicate with each other.
The help info for AutoRestore|Quarantine that you are looking for is here: http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/#procedural-steps
AutoRestore|Quarantine Manual File Editing/Uploading Procedural Steps
AutoRestore|Quarantine (ARQ IDPS) is a real-time file monitor that monitors all of your website files for any changes. When manually uploading or modifying files or folders with FTP use these simple procedural steps 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. ARQ is amazing, but it cannot tell who you are if you are manually modifying or uploading files or folders outside of your WordPress Dashboard – that is not possible.
1. Turn AutoRestore Off on the AutoRestore page.
2. Manually upload files or manually modify/edit files or folders.
3. Click the appropriate AutoRestore Backup Files button: Root Files, wp-admin Files, wp-includes Files or wp-content Files Backup Files button or run the Setup Wizards.
4. Turn AutoRestore back On.
BPS Pro Video Tutorials Link: http://forum.ait-pro.com/video-tutorials/
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