I had this happen with a new WD passport drive, and it turned out that a virus had gotten in, and made it appear like there were no files on the drive at all. But in truth, all the virus did was change the visibility of the files. The virus updated the visibility option on the root folders to "hidden", then updated the folder option that says "don't show hidden folders". Wow. And I thought I had lost all the files, and when I discovered what had happened, I had them all back in a few seconds.
The way I discovered it was when I went into the properties tab, it showed that 30% of the space was used. Then I tried something else, a search I think, and it showed all the file names as it browsed through the disk drive. That was when the light-bulb went off, and I realized what had happened.