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Why some empty folders can't be deleted ?

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dcunningham81 is right. These folders effectively take up zero space.

In fact, if you could find a way to keep these deleted, the trade-off would be Windows trying to find these many times a day. When it can't find them, it will look again and again, sometimes in different places, any time Explorer or something else calls for a list of directories.

You can even check on this sort of thing with something that tracks I/O calls (like Sysinternals Process Monitor) and see all the activity missing files and directories produce. You would probably never notice anything yourself, but it certainly outweighs by far the existence of a couple of zero-byte folders.