No, I never do that when updating a game. I just delete the entire folder and files and download the new one. However, in the case of Serenity, I just started playing your game like 2-3 days ago, so I never updated anything. It's a fresh install from scratch.
I did log onto Windows and the game runs just fine. It seems to be a Wine issue. What I'll do is go back to Windows, make a save for after the crash point, then back to Linux and load that save to see what happens.
Edit: Made a save and loaded it on Linux. Works fine. Rolled back the game and then went forward again. It got past the crash point with zero issue. Then I loaded the previous save I used and it crashed again. No idea what the issue is, but I can get past it now, so idrc. Thanks for the help though :)