Most of the time, the recompilation process of Apache/php with Easyapache with WHM/cPanel server will be effected the users’ .htaccess file. Most probably the entries like “AddHandler” will be commented state.
We can prevent the .htaccess file modification from the WHM tweak settings.
In WHM-> Server Configuration -> Tweak Settings -> System
Depth to recurse for .htaccess checks = 0