You need to create an AutoRestore single file exclude rule for your root htaccess file > https://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/#autorestore-exclude-rules
1. Copy the path to the file displayed in Quarantine. Example file path: /xxxxx/public_html/.htaccess
2. Restore the .htaccess (auto_.htaccess) file that was quarantined.
3. Use the Quarantine > Exclude Folders|Files Form at the top of the Quarantine page > select Exclude an Individual File > Enter the file path. Example: /xxxxx/public_html/.htaccess
4. Click the Exclude Folder|File button.
5. Turn AutoRestore back on.
Video Tutorial For How to exclude files or folders from being checked by ARQ: https://forum.ait-pro.com/video-tutorials/#autorestore-quarantine