Tool to Consolidate Data on Multiple Hard Drives and List Differences Between Filesets
To close out this question, I didn't really find anything out there already.

I ended up writing a python script that read all the files on the drive and saved an MD5 hash of each one in a database.

Then I created another script that would read the contents of the drive to compare and lookup the MD5 in the database to see if the file already existed. It's not perfect, but it worked.