With "invalid files and folders", I mean the problem, that occurs with robocopy, if you try to copy your userprofile and forgot to exclude Junctions with /XJ, at example:
I have never seen the bother in empty folders. They take up no space. But if a user wants them gone then thats up to them.
For test sake i just ran find empty folders and it listed 903 empty folders. Bothers me? Not in the slightest. Most of them are burried so far in my computer and places i would never go.
I dont know what most of them are, and i am not going to research hundreds of folders before i delete them.
Some programs require certain folders to exist, even when they are empty. Deleting those folders may cause these programs to stop working properly. Only delete folders that you are sure you do not need.