During the attacks, there was a considerable amount of confusion, however, the U.S. personnel did a tremendous job of reacting in spite of the short notice and difficult circumstances.
Some may recall that a number of USAAC fighters attempted to take off from Hickam and Wheeler, many did not make it. This can be said of several other fields across the island that also came under attack, but by some miracle, a small force of defenders were able to get airborn and engage, adding to several aircraft that happened to be airborn during the Japanese attack.
As far as this PBY is concerned, I imagine that if any PBYs were lost in operational incidents after the attack, it would have most likely been noted by a MACR and identified.
Here's a report from the commander of Kaneohe Naval Station (base of Scouting One) filed 1 January 1942, that gives us an idea of what happened that morning.
Pearl Harbor Attack: Patrol Wing (PBY) One Action Report