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Yeah, that might be what did it; depending on how you closed the game to retry the puzzle, it might not have saved properly. I don't know if there's anything I can do to help at this point, since it sounds like some of the saved data has been either overwritten or lost. I'm so sorry!

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No worries, thanks for such a quick response!

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I scrolled through some older comments and found a fix that worked for me - changing the 'respawn' value in the options.ini