Tim I agree the whole function is a bit complicated. There are cases when program knows which duplicate to delete, and there are cases where it does not. For example, if you have main archive, and there are file copies in other archives, you can delete all those duplicates with just one button click. However, if you have all your duplicates inside your main archive, program has no idea which ones to keep and which ones to delete. For example, there could be some meaningful folder structure, and if program will just randomly pick which copy to keep, that may break your structure.
However, if you don’t really care about your original folder structure and OK to go with yyyy-mm-dd, there is better solution for you. You can just import all your files into this yyy-mm-dd structure using this function, it will not only move files, it will also take care of duplicates in the process. I think this will be the easiest way for yo to clean up your archive.