To delete an extremely large number of files in Quarantine use the BPS Pro Xternal Tools (XTF) Form:
http://forum.ait-pro.com/forums/topic/xternal-tools-xtf-guide/
Delete All Files in Quarantine
Usage: If excessive files have been sent to Quarantine and you are unable to delete all the files in Quarantine using the Quarantine Sort|Search Feature, select the Delete All Files in Quarantine XTF Form option and click the Submit Xternal Tools Form button. If excessive files have been quarantined you can turn off ARQ and either delete or restore all files by selecting the Delete All File In Quarantine or Restore All Files In Quarantine XTF Form options.
For future reference, when manually modifying files (manual file editing, uploading files or restoring backup files) on your website use the ARQ procedural steps below.
AutoRestore|Quarantine Standard Procedural Steps when manually modifying files
http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/#procedural-steps
AutoRestore|Quarantine Manual File Editing/Uploading Correct Usage
AutoRestore|Quarantine (ARQ IDPS) is a real-time file monitor that monitors all of your website files for any changes. When manually uploading files with FTP or manually modifying files or folders on your website follow 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 files or folders outside of your WordPress Dashboard – that is not possible.1. Turn ARQ 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.
4. Turn ARQ back On.