I did a new fresh install of the previous version in C:\WebRatio as the installer suggests, not in C:\ProgramFiles\WebRatio where all my programs are.
Then, I started the ordinary updating procedure clicking on Help -> Check for Updates. It works, and I was able to automatically upgrade WebRatio to its latest version.
I did not go in deeper details, possibly the message "Cannot complete the install because of a conflicting dependency" is confusing, and actually the issue was bound to permissions in C:\ProgramFiles? I don't know the answer ;)