Help :( I have been having problems... (Newbie) :p

Hello people I have a WD My Passport & I would like to ask if my laptop can be damaged if ever I were to delete the back up in the hard drive improperly??? You know not using the software that they provided and anything… Because I stupidly deleted a file in my hard drive which I didn’t recognize then later remembered it was the back up file for my laptop… After this my laptop’s windows explorer has been crashing and the launch repair mode or something has been has been coming up before I turn it on and that repair takes soo long but it just repeats the process afterwards in my next startup… 

& now I wanna make another backup but now it says that there is 0 files to back up. cuz it considers the whole thing as system when in my previous back up it was divided into lots of sectors like documents; pics; movies; music and system. 

Anyways can anyone please tell me what is the problem and PLEASE provide a solution :frowning: