A while back I wrote a backup application which allows you to compare folder structures on different disks. I still use it, and it’s useful for keeping Dropbox folders, USB keys etc. in sync.
I haven’t written much documentation for it, so you’ll just have to try it carefully. Best to have a go with some files that aren’t utterly vital, as it’s perfectly possible to delete lots of stuff. 32 bit MSI, and 64 bit MSI available for download.