When uninstalling a mod component messes the game.

Hello

I gues this is a topic with a silly question, but i really need a fast confirmation of this.
Recently i tried to uninstall a g3 tweak pack component and something wierd happened in the weidu setup messing it up.
Of course i've made a backup folder with the whole game.

My question now is: should i UNISTALL the game and then copy the backup into the directory where it was, or should i DELETE MANUALY the orginal folder with the game and then copy the backup into the directory where it was?

Again sorry for the silly topic...