You should look over the list of files to be deleted to ensure that you do not delete anything that should not be deleted. Neonix Remove Orphans relies on Dreamweaver to accurately identify orphaned files.
If you have reason to believe that the list of orphaned files is not accurate, try the following:
- Select a different site, then return to the original site
- Recreate the site's cache
If there is an .htaccess or .htpasswd file that you do not want to have deleted, then add "htaccess" or "htpasswd" to the ignore list - be sure to delimit them with commas!