So do you think maybe the place was flooded to kill off a set of "failed lab rats", once? Or that... Maybe one of the people who worked on renovations saw what it was being used for, and found a way to leave clues behind so we'd have a better chance of figuring out whatever it is we need to figure out?

[ Though, that leaves behind another question: Whether they're pointing the way to a second win condition or something else entirely, why the song and dance? Why not just tell them what they need to know? ]