The context makes it all a bit more complex but the overall process of identifying folders and counting files would be much the same. A few added steps.
The project that you have in mind should be thought out in advance. Planned out step by step in a manner that allows you to stop at anytime if and when necessary. No large scale "enmasse" efforts that could go astray and not be stopped.
Not familar with that linked product so will defer to others who may be familar with it.
Additional thoughts.
1) Be sure the various photo directories are all backed up away from the current host computer and drive(s). Verify that the files are both recoveralble and readable (viewable).
2) Moving files is risky. Use copy and paste. If something goes wrong during a "move" the file could be lost in electronic limbo.
3) Be wary of third party software: it could be buggy, corrupted, contain malware, or otherwise cause system problems.
4) Do not put any files in the root directory. Create a separate target folder and put the culled images into that folder.