I put myself in the GOG beta branch, so this could be something that the latest beta patch introduced. However, I have no frame of reference because I had not reached this stage of the quest until today.
I am doing the The Lighted Path quest. I rather readily found Bosc's ship, boarded, took out the upper-deck crew then went down and managed to talk Bearn out of suicide. My quest updated to take Bearn to Hasongo. That was fine, but I wanted to take care of a few bounty quests nearby before making the journey, and I did so.
Back in the Deadfire Archipelago map, I see a stationary Bosc's ship where I had previously boarded and rescued Bearn. If I board it, I am treated to what I presume happens if I took too long and everyone, Bearne included, committed suicide. Going below decks reveals the deceased Bearne (despite me rescuing him earlier) and completes the quest.
This is not game-breaking, obviously, because I was able to reload from before I boarded the ship again and I was able to finish the quest in Hasongo (and the abandoned Bosc ship did disappear after that), but it is clearly not as intended.