Hi Eliot,
I have tried the steps you mentioned, unfortunately it did not work.
I have read the documentation from Ardusub that if the main LED on the pixhawk did not change from blue to green, then a valid position and lock is not detected by the autopilot 
. And the LED in our pixhawk keeps flashing in blue.
We have also turned to the companion page of the waterlinked driver, it did not show the sign of ‘Scanning for Water Linked underwater GPS’, (which was mentioned in the link of Waterlinked UW GPS Gen2 not autostarting Ardusub driver), every time I press the restart button, the website remain unchanged, so I am not sure whether the driver has been restart.
The link (Waterlinked UW GPS Gen2 not autostarting Ardusub driver) mentioned that the problem is only with the customer of G2, may I know if the problem has been solved now? Or is this the main reason that I could not get the GPS detected by the pixhawk?
Thank for your help!