When I got to the server room in the beginning of the game I didn't prepare the hatch on the door so that it would stay open. Does that mean that I can never get in, or is there another way of doing it?
Just repeat whatever steps you took to get it open the first time and try again. The game will never let you end up in a position where you would have to reload. Another good tip to keep in mind is that whenever it seems like you're stuck remember that you always have your scythe at hand.