There is, of course, an option to give a warning when files are to be replaced (files already exist, overwrite? rename?), but there´s no such option for folders, in case they are moved to another place, where folders with the same name already exist. An additional option in the -> file operations -> "confirm overwriting of existing folders" would be useful.
Folders aren't replaced though, their contents will instead be merged.
That´s alright, but an extra query would be good.