After experimenting for a bit, I guess the answer to your question is "Yes", because:
- After managing to make the Creaker go, its entry on the entities list is now green
- If I quit the game and start it again, the Creaker entry is still green
However:
- If I select the Creaker, I can go through its process all over again (though that's probably the intended behavior)
- If I go back to the menu in the midst of a conversation with an entity, my partial progress isn't saved (again, that's just probably an intended feature and not a bug)
- Until I "beat" an entity, no save file is created at C:\users\MYUSERNAME\AppData\LocalLow\Shakles\Totem, and the same "file not found" exception that I experienced with the Linux build, is also thrown to the Player.log file
So in conclusion, I'm no longer sure the "file not found" exception was relevant to the crashes with the Linux build... :\
PS: The game was rather hard to play because I didn't get a little dot in the middle of the screen acting as a crosshair, but that could well perfectly be a Wine issue...