I've been selecting 1 or 2 directories at a time to analyze, as I think that's the best way to approach cleaning up over 2800 files.
It seemed to work ok when I selected the first 3 directories. It did move the files, but gave an error for each one;
Warning: mkdir(): File exists in /home/bwsn/public_html/wp-content/plugins/wordpress-uploaded-files-cleaner/wordpress-uploaded-files-cleaner.php on line 187
Move file /2012/10/KERR-PUTTING_crop-285x280.jpg : done
When I go back to do it a second time with a different directory, I get inconsistent results. One time it might not show ANY files, even though there are many there. Next time, it will let me select the unattached files, but when I push on "move selected files" it doesn't do anything, just takes me back to step 1? This particular directory has 1800 elements. Could that be why?