The EMH backup module was discovered in 3074, and The Doctor had to defend himself from accusations of committing war crimes in 2374, although the simple fact of his holographic nature was enough to make the Kyrians question what they had known, ultimately allowing The Doctor to debunk the utterly inaccurate revisionist history the simulation taught. (VOY: "Living Witness")
"From what I can tell, The Doctor was telling the truth, at least about one thing: he is a hologram. A backup program. We always knew he was an artificial lifeform, but we thought he was an android. If we were mistaken about that, I wonder if we might also be wrong about Voyager itself."