Ah, what I suggested in comment #18 would only re-create "system" connections (such as desktop, audio-playback etc) provided by snapd, but the other problem is with gnome-3-28-1804 and gtk-common-themes content provider slots. For those, removing and installing them back should re-create their auto-connections, so try this:
As for the actual root cause, I fear it will be very hard to understand what went wrong without "snap changes", which unfortunately got pruned already.
Ah, what I suggested in comment #18 would only re-create "system" connections (such as desktop, audio-playback etc) provided by snapd, but the other problem is with gnome-3-28-1804 and gtk-common-themes content provider slots. For those, removing and installing them back should re-create their auto-connections, so try this:
$ snap remove gnome-3-28-1804
$ snap remove gtk-common-themes
$ snap install gnome-3-28-1804
$ snap install gtk-common-themes
As for the actual root cause, I fear it will be very hard to understand what went wrong without "snap changes", which unfortunately got pruned already.