So, I assume you mean empty the folder and then copy the new ones in?
Or did you copy the files and merge, then delete any extras?
I did the first method, deleting the files first, and then copying over, but that didnt work.
Edit: Did you have the catalog manager/game open when you deleted/copied files?
Edit2: Yeah, seems like keeping the program open as you delete the files is a necessity. You could do with specifying this in your guide.