My Win 10 has never 'seen calibre as a threat'. Are you sure its Windows telling you that and not some 3rd party Security Suite.
Does your son have any evidence that the Windows update 'messed with calibre'.
There are about 3.08M
active calibre users, more than 80% of them use Windows, that's ~2.46M. According to NetMarketing, Windows Version 10 has about 20% market share. Let's be conservative and use 10% - which means 246,000 calibre users are on Windows 10. As far as we know you're the only one where a Windows update 'messed with their calibre'.
See
Usage Statistics for calibre, and
Operating system market share
BR