Working on update: 100% complete. Don’t turn off your PC. This will take a while. Your PC will restart several times. All your files are exactly where you left them ;)
I'm baffled by people still claiming "desktop Linux hasn't arrived" when they put up with this shit.
If you don't enable this feature (which isn't enabled by default in Debian) you won't have this problem.
But they do have an excellent solution to the whole updates debacle: Install them in a separate location, initialise them when booting or when they're finished installing, and delete them when they're inaccessible from a few standard locations like /boot or /proc.
I'm sorry, you say that as though Linux Desktop doesn't have a giant pile of its own shit to put up with. Windows definitely isn't perfect, but I'll still take its shit any day over Linux Desktop's.