This was the approach I originally was considering (to do in-place duplicate deletion), but eventually gave up due to the impact of "undiscovered features" in my code.

The approach I've settled on which should work for most people is to establish a new library, with unique copies of each of your originals, skipping exact SHA matches and invalid files.

In your case, though, you'd run PhotoStructure in its "don't copy into the library" mode. Once it finishes scanning your drives, you can run a simple SQL query against your SQLite db to get a list of duplicate files. That query will be in the FAQ.