Remove paper from parent, but not child folder

I’ve switched to using folders instead of labels after many years. Assume I have a folder with multiple subfolders. I want a specific paper to only be in one of the subfolders, but not the parent folder. The only papers that remain in the parent folder are those that don’t belong in any of the subfolders. Think of them as the unorganized papers. So, how do I remove an instance of a paper from a parent, but keep it in a subfolder? Deleting directly from the parent also removes it from the subfolder.

I prefer exactly the opposite behaviour: thinking of folder as a taxonomy. If a paper does not belong to a parent folder, it cannot belong to a subfolder.
Maybe an option to toggle between the taxonomy/filesystem interpretation of folder may help!

Unless I’m mistaken, folders function mostly like labels in disguise, so to remove a paper from the folder you would add/remove the folder from the paper just like you would a label.

Deleting a paper would be a wholly separate type of action which removes it from your library and places it in the trash.

To have a paper in both a parent and sub-folders, one would have to add all the parent folders to the paper.

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@Mark_Pezzo like @Jason_Jensen points out, folders are basically masked labels so papers can exist in subfolders without being added to the parent folder, or be deleted from parent folders and remain in subfolders. Here’s a video demonstrating as much in a sample library.

Correct. And this is extremely time consuming (and error prone) if I have many nested subfolders and would like to use them as a taxonomy.
Any workaround available to have a paper appear in an entire subtree, without having to manually add to all folder levels (and maintain consistency manually)?