Cleaning master files

I know this should be very easy but I just dont get it

After cleaning files , the files stays in *overwrite* and I cant get it out , its not a backup because when i delete it , it gets deleted in the load order aswell
I tried creating a new mod from this file , naming it the exact same but then it goes to the bottom of the load order in the left pannel.

Leaving it in overwrite seems okay as MO doesnt pop any error notification , but I dont think I should leave it there 

I followed everystep of the tutorial video about cleaning master files , but I end up with , for example , update.esm and TESEDIT BACKUP (something like that) in *overwrite* and in the video theres only TESEDIT BACKUP in there


I know it is only recommended and that i could still play but I dont wanna see my game breaking up on me 

Anybody knows what to do ?

Im on windows 10
SPM 4.4

You need to manually move them from the overwrite folder back into the data folder and then refresh MO and check they are in the correct order.