Welcome to the forum @Nutri
Does “those files” mean those you want kept, and “that backup” mean the one with extra folder?
If so, that’s a good way to take advantage of B2’s free-uploads pricing, but it’s more upload time.
Alternatively, removing the one non-interesting folder can be done using The PURGE command.
How to delete some folder or/and files inside each backup version gave some directions for that.