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!
How are you launching the exe with WINE? Try doing it via the command line if you aren't already. That way you may get some more information about why it isn't working. Its as simple as
wine path/to/your/exe
You could also try something like Bottles, which will let you use possibly newer versions of WINE without modifying your system's WINE.