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Why some empty folders can't be deleted ?

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Bruce Epper

In that case, the key is that they come back when you boot normally. So, delete the files/folders in Safe Mode, run CCleaner to clean up the registry, and then reboot to see if they come back again. Since their registry references should be gone, Windows should not attempt to resurrect them.

You could also manually scan the registry to find references to these folders and remove them yourself.