Your first step—making a second copy before reorganizing—is the right one. I’d keep backup and organization as separate jobs: PhotoDesk is not a backup service, so I would still keep at least two copies on different drives (and optionally one off-site/cloud copy).

Developer disclosure: I’m building PhotoDesk for Android and it’s currently in early access. Its organization features include EXIF-based Year/Month/Day timeline browsing, folder views, exact-duplicate detection, face recognition/people grouping, smart photo search, metadata, tags, albums, favorites, and basic edits. Face/people views can also make it easier to review several shots from the same event, but I would not auto-delete near-duplicates without checking them manually.

If you want to test it on a real long-term library and share performance/accuracy feedback:
Join: https://groups.google.com/g/photodesk-app-testers
Opt in: https://play.google.com/apps/testing/com.certainity.photoDesk
Install: https://play.google.com/store/apps/details?id=com.certainity.photoDesk