Imagine you are transfering large amount of data because of system migration of whatever. You start copying or moving of many folders and go away for half a day thinking that it will be done when you return. You get back and WTH! Copying stopped on some stupid question like "cannot read this one file", skip? Half a day wasted because the operation just couldn't continue because of one totally unimportant problem!
So my suggestion is very simple: don't pause the operation when some problem is encountered! Just continue with the rest which does not have a problem and just queue up the prompts for the user to interact when he gets to it. This way everything that has no problem would be done and all those "are you sure" or "skip" type of prompts would not stop it.
There could be some global option to enable/disable this like "don't pause file operation on error/questions"
Typical example when moving a folder with photos: are you sure to delete hidden file thumbs.db? Jeez that file is there since Windows XP and it's absolutely not important even though it's hidden, so any questions about it can be automatically answered yes
