One thing you can try is to ignore the contents of the Duplicate folder (it doesn't take up any additional space on the drive) and try a 3rd party duplicate finder. There are only two that I can recommend. You want an app that will identify the potential duplicates, put them in an album or mark them with a keyword for easy retrieval and deletion by you. You don't want one that does the deletion itself for obvious reasons.
I've run tests on the these two apps with the following results and found them to be safe to use:
PowerPhotos - $29.95
PowerPhotos is the iPhoto Library Manager version for Photos and is very powerful. Although more expensive I would recommend it as it has more capabilities than the others like the capability to merge Photos libraries or copy photos, both original and edited versions, along with their metadata between libraries.
PhotoSweeper - $9.99 - Demo version available.
PhotoSweeper compares bitmaps and/or histograms so it can detect duplicate images even if they have different file sizes, file names, image sizes and capture dates.
You can try the out and see if they give you any more control over what it considers duplicates. PowerPhotos is by far the more powerful of them. can scan photos in libraries without opening Photos and is also the premier support tool for Photos.
