I was looking to store the files in their native format on both the external hard disks (I wouldn't use some kind of backup software to image one hard disk onto the other one, this feels like a lot of reading and writing to me, when the actual differences may be relatively small between them) and was instead hoping for some kind of software that would be able to differentially identify the differences between the two USB disks, and then transfer just those files over.
FreeFileSync does this exactly.
Point it at both folders (ex E/Movies and F/Movies), and click to compare the two folders/subfolders. It will tell you exactly what is different between the two. You then have the option to make them the same, in either or both directions.
There are multiple ways to do this automatically, but I prefer the on demand concept. Sync when *I* want to.