I've had this problem crop up too. There are some utilities that are easier to use, but I recommend
Cygwin
It's sort of like using Linux bash, but in windows. Open the prompt as admin. Once you're in the prompt you do the following:
#cd <drive letter of kobo>: <--- ex. cd D:
#ls -al <---- tells it to list everything, including hidden folders
#rm -R <folder name> <---- deletes the whole folder. You have to put a '\' before the space character if the folder name has spaces in it.
I'm not quite sure why it works the way it does, but I don't see anymore hidden folders.
Hope this helps.