Figuring out the size of data on an external harddrive

Question

I have an external HD, a seagate backup plus slim 2TB. The filesystem on it is exfat. It has a single partition. I want to create a new partition table for this device, so I can use different partitions for different purposes. However, only about 1.6 TB of the drive is free. I wish to make sure that I do not accidentally delete anything, so my plan is to copy the files on the external drive to my desktop, create a new partition on the external drive, and transfer the files back to the newly created partition. When I check the total size of the files/folders by running du /media/external_hd, I get a 416 G usage. When I do run the du command on the top level folder into which I copied the entirety of the external drive, I get 364 G usage. I might be paranoid, or maybe it has something to do with the block sizes on the two different filesystems, but how can I make sure that I am not leaving any files/folders behind as I am going through this process? I copied everything with cp -R so I don't think it is a hidden files/folders issue? EDIT: Also this occurs on MacOS 10.13 High Sierra btw, my apologies for the linux tag. I usually use linux and hence the confusion.