|I don't have any idea on earth how or why it happened, but I have a suggestion for something which may get your folders back.|
Determine something you would not mind losing as much as other stuff...if there is one folder you could stand to lose more than the others, try it on that. You may lose it, you may not.
Open Folder Options in Control Panel. On the View tab, make sure the following options are set the way I say:
-Hidden Files and Folders: "show hidden files and folders"
-Hide Extensions for Known File Types: unchecked
Go to the external hard drive, hit F5 (for Refresh) if it was already open, and you may see that the "folders" now have an extension of some kind... a few letters following a period in the folder name. Find the "folder" that you would not mind losing very much, rename it, and in doing so remove everything after the period including it. When asked, confirm that yes, you do want to change the extension.
If it becomes a folder again after doing this, you have the solution to fixing all of them.
If it does not - STOP. Do not do anything else. leave it until someone else replies here, because it means my solution did not work, and anything else might risk damaging your data.
Hope this helps, and does no damage.