For the files *.mkv the default app change order.
I have vlc first like this: vlc.desktop;mpv.desktop;com.github.Bleuzen.FFaudioConverter.desktop;
But after each upgrade, vlc become last and FFaudioConverter first.
Same with the defaults apps.
web browser: I select firefox then others. but firefox switch to last every upgrade.
email client: thunterbird switch to last every upgrade.
map: openstreetmap switch to last every upgrade.
Software updates never ever change anything inside your $HOME directory.
If anything, this is confined to the system wide config in /etc
I have here a almost pristine installation of Plasma in a VM.
It never had or saw any video or audio file.
and: ~/.config/mimeapps.list
does not even exist here.
If something changes on you inside your $HOME without you doing it - it has got to be some “bug” in KDE/Plasma.
Maybe changing the file associations by right-clicking on the file => Properties => Open With => Change isn’t creating a permanent change to the file associations. Try changing them via System Settings => Applications => File Associations (and make sure you save the changes by clicking the “Apply” button at bottom right of the screen afterwards).
Any time you want to open a file via the file manager and do not chose the default application, but another one instead, this change is reflected in that file - if the file isn’t there, it gets created.
That is how it is in Xfce4 at least.
Did not test this in Plasma yet but I’d think it works the same way.