Sometimes it helps to use the Shutdown and Install Updates. If you open your start menu, the shutdown icon will have a special icon over it. It will makes some changes before it shuts down, then after you manually boot back up, it will finish up. It's usually required to change files that are in use. Also, I think you might need Automatic Updates set to automatically download and install at specified time for the option to show up. I don't know why windows update isn't smarter about this, but I've had failed updates before and this has always fixed it.
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