There is no upgrade path between the original and newest versions of Niente. Niente Version 4 is installed alongside Version 3: it doesn't replace it. As a small convenience, the shortcut or soft-link /usr/bin/niente is re-pointed so that it launches /usr/bin/niente4.sh (the version 4 executable) rather than /usr/bin/niente.sh (the version 3 executable). This means that after installing version 4, the bare command niente issued in a terminal session will now launch version 4 of the program. But if you wanted specifically to run the earlier version 3, you could still do so by typing the command /usr/bin/niente.sh.
It is recommended that, to avoid potential confusion, you manually remove Niente Version 3 from your system as soon as you are happy that Version 4 is your FLAC integrity checker tool of choice. That's done with the following commands issued in a terminal session:
cd
rm -rf .local/share/niente
sudo rm -f /usr/bin/niente.sh
It's not a requirement to do this, however.