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Toreth - try using right click Restore Previous Versions on the file in question - maybe you'll get lucky.
And reconfigure Windows Update as shown, then
you will be in control of when WU downloads, when WU installs, and when WU restarts.
The default setting assumes that entirety of the planet's population lives in the USA, that they can all afford to leave their computers running 24*7, and that they're all in bed at 03:00 in the morning
IMO auto-installs of anything are a menace - but most vendors, including MS, do NOT force you to accept being force fed. Although some of the majors in the Valley try mighty hard to do so.
BR
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I also moved to Devices because its an OS issue - in truth its probably a Sigil issue, if the OP had been using the calibre editor then maybe the file would have been recoverable from a checkpoint - dunno if that's true as I never tried it