I noticed this morning that one of my users (actually would be several, but this is the first user I troubleshooted) had 3 folders missing from the explorer view of a document library. They were oddly named with the first character being an underscore(_).
So digging a little deeper, I smacked my forehead and remembered that underscore is Windows’ way of determining whether or not a folder should be hidden. So I copied the folders to my desktop, deleted the folders on SharePoint, renamed them without the (_)underscore, and put the files back.
The user can now see the folders.