I thought the line was, "Never mind that..." as in, we don't have time to investigate the mystery of who Dr. Shin is right now. My guess had always been that the director of the archive was this Doctor who put the place into lockdown on his personal code, and so the AI inside has been waiting for him to return this whole time; the last thing he told it was, "I'll be right back," or something along those lines, and so when the door opens again, it responds to the person who opens it as if they were the Doctor. I suppose I'm not that paranoid.