I can think of a way to do this under Unix/Linux (or Cygwin), but it onvolves the command line.....
Basically, you do something like:
find <name of top level folder> -print | xargs sum | sort > listofbooks.txt
Then you search for lines in listofbooks.txt that have the same checksum entry - they are probably, but not definitely, duplicates. If you want I can make this more robust and automated - it's what I'm going to have to do myself, but not for a week or so. If you want I can post the script once I do - but it will be a Unix/Linux script.
There's probably a way to do it using PowerShell too, but my PowerShell skills aren't that good yet.