The same happens for me all the time. I have a an external USB drive with a lot of nested folders. I use the list view on the right pane. I haven't seen it happen on the left pane though, even for big folders.
I didn't delete anything by accident yet, but when I browse through my folders while searching for something I often expand a folder, see what's inside and collapse it again. If I do it fast enough (and the USB drive is slow enough) I miss some folders. The (Empty) string sometimes stands there for about a second, so I would consider it as a medium bug because it really annoys me ;) -- Nautilus list view calls non-empty folders "empty" while they load https://launchpad.net/bugs/42690 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
