Lightroom’s Folders panel can show only the folders it currently knows about, so some child folders may appear “promoted” instead of nested under their parent folders. This doesn’t necessarily mean the files are misplaced on disk.

To make the panel better match your actual drive structure, right-click a folder in the Folders panel and use Show Parent Folder (repeat as needed). That tells Lightroom to display the higher-level folders above the selected folder, rebuilding the visible hierarchy.

So the difference you’re seeing is usually a display/navigation issue in Lightroom’s folder panel, not a filesystem problem.