When is an empty folder not an empty folder? When it's located on SharePoint of course! The folder may appear empty in SharePoint, in Explorer view and in SharePoint Designer. Attempting to delete the folder results in the following message:
"The file is currently checked out or locked for editing by another user."
More than likely, the document library requires check out and may have versioning enabled. Someone uploaded files to the document library, but never checked them in. So, there are files in the folder, but only visible to the individual that uploaded them. To locate these files:
All the files that have never been checked in will appear. Select the files and then click "Take Ownership of Selection". The files will now be visible in SharePoint and can be deleted or checked in. Deleting the files will allow the folder to be deleted.