I have just created a new testing environment on my SiteGround account and I'm having issues.
i used Akeeba Kickstart to restore a backup from production to a new folder and a new database - at first I'm not able to log in due to the Backend Protection - I renamed the .htaccess file to .htaccess.old - after that I can log in to the backend.
But then I get a 404 error when accessing the front end. Even when I rename .htaccess.old to .htaccess the front end 404 error is still there.
This is the first time I have tried this process since SiteGround changed away from CPanel to their own Site Tools so maybe it's something to do with that. In the past I haven't had an issue with the Backend Protection.
The backend protection only affects to backend; it has no influence in frontend. Did you delete the .htaccess or did you remove only the backend protection? Remember that you need a .htaccess into root folder if sef is enabled; if you don't have it you will get 404 errors on navigation.