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.
I've also noticed that when I changed the various items from "No" back to "Yes" and click "Protect" SCP writes a whole new set of SCP instructions below the previous set. In some cases, this results in 3 or 4 repetitions of SCP instructions in the .htaccess file. What would be the correct procedure to avoid this? Should I just start with a clean new htaccess.txt file from the current Joomla versions and re-protect? Or is there some other method you suggest? (I guess I assumed SCP would read the file and only add the updates to it.)
The best method is save the changes, delete the .htacess (there is a button to do that) and then click on the 'Protect' button. I tried to implement a reliable way to change settings but I didn't find it.