problem removing duplicates in a folder.

I have a large folder with with multiple subfolder. There are too many duplicates which I want to remove.

There is a program which I have been using for removing duplicates.  However it is not solving my problem.  The reason for this is that the duplicate photos are not in the subfolders but are present in the bigger folder. I have carefully gone through all of the subfolders and removed the duplicates in them. However there are still many duplicates to remove. If I use the duplicate program on the top level folder it will show all of the duplicates, but there is no way I can find which will show the location of the duplicates. I only wish to remove to duplicates that are lying all mixed up in the outer folder. I have tried to put these photos in a separate folder in the database, but Lightroom cannot see it and thus I cannot sort through them separately from the photos that I have already sorted out. I have thought of deleting the big folder from light room and then reimporting the folders one by one and then finally the random outer photos. Is that the way do solve the problem?   Thanks.