Are you on BTRFS? If so maybe you could restore to a snapshot prior to the apt upgrade?
I'm not very familiar with Debian, but perhaps there are official "groups" of packages that comprise a set of softwares, like KDE. Perhaps you could re-install that group, if it exists?
You could also create a new user, log in as that user, and see if the issue persists. If so then you'll know it's a system wide issue. If not, then maybe you could migrate to the new user?
Good luck!
Delicious in Dungeon!