It's a long time sine I last used Ubuntu. It used to be very easy to install SH3D (just unpack in a directory of your choice), but after a few updates it was almost impossible to update a program if it's not in the repository/appshop. Reason why I switched back to W10.

You need to find the (hidden) directories where SH3D is installed. Search for the executable of SH3D and replace that with the new one. As far as I remember that should be enough.

H