This is the type of thing that I find so frustrating about KDE Discover (and Gnome Software). They abstract the user from the native tools of any distro, and frequently fall short of perfection in their coordination with those distros.
I've upgraded Fedora something like 20 times using dnf on both Gnome and KDE Plasma DEs, and I've never had a problem like the one you encountered.
But just in case, I do always do the backup thing first. :)