It was a very silly mistake of mine. I am now at village for EID vacation and yesterday I was getting very slow speed with GrameenPhone. For some maintenance task, I thought to access the cPanel with my mobile. While accessing the "Legacy File Manager" of cPanel I touched a wrong menu unintentionally and the destruction happened.
The issue arises because we may not need the same permission for the files as like the directories. Take a website as example. Generally website files have 644 permission and directories have 755 permission.
Here you can change your permalinks as you like and make it SEO friendly. You will find here 4 predefined permalink structure. You can set them. There's also a box called Custom, You can define your own permalink structure here.