Well, if you use F: as the source, and tell Windoze to overwrite existing files in favor of the source, then it will dupe F: onto D:. However!
The only time this will happen is if the source and target have the exact same filename. If you have changed the filename, you will have a whole lotta dupes.
If you have different files on D:, then they will remain unaffected.
I have a similar setup in that my music (125,000-ish) are on a Passport (PLUG! Luv em!) nd any new file that have not been edited for tag data/vetted for dupes reside on my home directory in /Music. Housekeeping becomes exponentially more difficult with any increase in total number of files.
You may wish to try a duplicate file finding utility like
Easy Duplicate File Finder
or something from Sourceforge or Tucows. I have no experience with these, so caveat emptor!