OK, after watching the gameplay video, I think option 2 is correct ("shuffled into the deck"). This is because in the video, the second donsol reappears in the next room right after it was escaped in the previous - this would not have been possible in option 1.
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Oh that's quite interesting.
When I play with physical cards, I just shuffle them and put them at the bottom of the deck. But the game puts them in the deck and shuffles the deck. I can't quite tell what's the better option for the narrative aspect of the game. Shuffling the deck means that the monsters move to a different room, shuffling the remains of the room and putting it under deck means that you eventually return to that room.
I agree that gameplay-wise shuffling into the deck is better. Otherwise, becoming good at the game means having to memorise the positions of all the cards you have escaped! I'm not sure I find that fun :D
From a narrative point of view, I don't find it a problem - you could say that monsters are roaming. In any case, 'put at bottom of deck' doesn't ensure you get the same rooms, since you don't always escape a full room. So the current narrative of "returning to the same room" is sort of broken already.