So what I did was play the game like normal, while saving regularly. I saw the scene of Gunnar being kicked out, shortly after the bilge pump scene. I loaded my most recent save point and played around a bit to confirm that, yeah, I need to do the bilge pump puzzle before Gunnar is kicked out. Also, I need to visit one of these places:
- Soren's cultural center
- The lighthouse
- The ice caves
- Magnus' house
I'm not sure what any of those places has to do with Gunnar. Maybe the game figures that time progressed, since you left town and came back. And...for whatever reason, Soren's cultural center counts as "out of town". I'm not a programmer. I don't know.
After this, I loaded my previous save point! That save point was after looking through Dagny's luggage. From there, I tried the same strategy. That is, I went directly to the bilge pump and solved that puzzle, then I took a trip to the lighthouse. That triggered the scene of Gunnar's ejection.
This begs the question: what triggers the scene at the bilge pump? I did more playing with my save files, and it looks like the bilge pump scene occurs, once you take the photo scraps from Dagny's luggage.
As for making Gunnar reappear after this, I had to solve the puzzle in the crow's nest by Soren and the Venn Diagram puzzle. Not sure why, but it worked for me.