I use Roadkil's Unstoppable Copier when I see this happen.
It has a better copy routine IMO than Windows File Explorer.
Windows 10, when I try to copy a folder containing subfolders from my computer to a USB thumb drive, it appears to copy correctly BUT when I review the thumb drive all the subfolders are empty. Yet when I check the properties of the thumb drive it indicates that the data is in it even though I cant get to it, as all the subfolders are shown as empty.
How can I do this without working around it by first copying the files that were contained in the subfolder to the thumb drive and then transferring them onto a folder created on the thumb drive ?