Hello pauljurczak
Firstly, managing Flatpak application on the command line is not difficult. After you have installed the Flatpak basic framework (which has to be installed before you install individual applications) read the short man pages for Flatpak.
You may find these pointers about using Flatpak helpful:
- ignore the parts about LibreOffice off course.
Secondly, Discover. If you are not running KDE I do not think you should install this. I can only see it leading to problems (if I am thinking about the same 'Discover' you are writing about).
You say you need the latest version of Okular (which I also use on occasion) - would Master PDF Editor be an option for you?
And finally, to get your system working correctly, you may well be better off doing a new installation of the Ubuntu-Mate release concerned.
I hope some of this helps you get going again. 