Not deleting ALL photos from disk

I've been doing a tidy up of my catalog. I started by marking 'rejects'. Then deleting all rejects, and selecting 'delete from disk'. The photos dissapear from Lightroom. I then removed empty folders.

However, when look via Windows Explorer, not all the photos and folders have been fully deleted! Some have clearly gone, as requested, but other pics remain.

I suspect this may be linked to either deleting across multiple directories and/or subdirectories simultaneously.