I did look at you screenshot.
No, it has nothing to do if they were empty or not originally when moved. You have the plain yellow user folders Music
, and Videos
without the "My" now because something went wrong or a mistake was made while moving them leaving you with duplicates there like in the warning under step 9.
I understand what you are saying, and not wanting to do this if it's just going to happen again. If you restore the default locations
and move them again afterwards, then you should no longer have the duplicates afterwards. Give it a try to see.