This is weird, but every so often when I'm checking a site's .htaccess protection in Securitycheck Pro, various items which were protected are set to no and the green bar is not displaying meaning it hasn't been applied to the .htaccess file. What might be the cause of this?
The Malware scan doesn't reveal anything.
That means the .htacess file into root folder has been modified. Did the file integrity report any change? Did you do any change in the server like changing PHP version? Sometimes that overwrite the .htacess.