I updated the companion software successfully to version 0.0.31. I then tried to update to the sable release of ArduSub via the Pixhawk firmware update section by pressing the stable button. It appeared to work, but now that ArduSub version is showing as “not found”. I downloaded the firmware and uploaded it manually via the web interface and the Pixhawk firmware update section and that did not work either.
If rebooting the vehicle does not re-detect the Pixhawk then most likely the update did not fully complete, and it is not starting up in bootloader mode which the Companion Software cannot detect. You should be able to restore functionality by either
Plugging the Pixhawk directly (via USB) into a computer running QGroundControl, and following the manual flashing instructions, or
Flashing BlueOS onto the SD card of your onboard computer (to replace the Companion Software), and updating to the latest 1.1.0-beta release, which is capable of detecting and updating a Pixhawk even if it’s in bootloader mode