The Water Linked instructions specify you need at least Companion 0.0.22 for their GPS to connect, so you’ll need to update the Companion software.
Given this, I’d recommend you try the direct flashing method of installing new Companion software. That unfortunately requires opening the enclosure to access the Raspberry Pi’s SD card, but if your wifi/internet access isn’t working then you don’t really have other options. There are some steps in this comment for opening the enclosure, if you haven’t had to recently.
While it’s open, you can either connect the Pixhawk to your topside computer and flash on a new ArduSub, or once your Companion has the latest software you can connect it to wifi and update ArduSub on the Pixhawk via the Companion web interface 