Did you reconnect the Pixhawk to the Companion computer before trying this?
If the web interface System page is showing the Pixhawk1 in the Detected Devices section, and showing 4.0.3 as the ArduSub version then that sounds like it’s operating normally, in which case you should verify QGC autoconnect settings, check MAVProxy, and possibly reset MAVProxy options and try restarting your computer, all of which are suggested in our troubleshooting steps.
If those aren’t helpful please send a screenshot of the System page from the Detected Devices section down to the ArduSub version section, and another screenshot or code-block of the output of the Check MAVProxy step 
Do you know which QGroundControl version you’re on?