Yeah, it happens to me from time to time when I forget to close Calibre. Pretty annoying but that how windows handle updating a running program.
However, the next release/installer will contain some warning if the installer detect that Calibre is still running, and will give the user the opportunity to close the program before continuing and having an unexpected reboot.
https://github.com/kovidgoyal/calibr...d2e8bd33132ce1
thanks Kovid