The ".vbs" indicates a Visual Basic Script file, quite likely something that the trojan installed and your virus checker removed. The "1 KB" may just indicate file size, about right for a directory.
If the files are all OK but the directories wrong, can you just grab all the files and format the thumb drive? That's what I'd want to do, but it is a little inconvenient if there are a lot of files.
Another thing worth trying is to see if the disk is readable with a different OS. A Linux machine or a Mac may show it differently than a Windows box.
For future use, look for a drive with a switch that makes it read only. Those switches used to be standard, but are now rare. One brand available in China that does have them is Netac; I have several. Mine are all 4 gig and finished in black & white, but I bought them years ago so you may find differences.
Before you insert it in a dubious system (e.g. anything at a Chinese school), move the little switch to make the drive read-only. Any attempt by evil software to write is then blocked at the hardware level. Your drive and your own computer are completely protected.
Of course, if you need to have students give you files, e.g. for marking, this is not enough.