I am not sure if this will completely solve your problem but I am hoping it will save you some time for the most part.
I have created an application which works in a similar manner. The application Sorter functions by grouping files by their extension ie pdf together but separate from docx. There is also an added option which can group documents together but separate from videos and audios. The good thing, for your case, is that you can determine the destination of the files; plus it has a recursive function which checks into subfolders and their subfolders and sorts/groups the files relative to their initial location. Try it out and see if it can help.
