The USS Atlantis (NCC-4804-D) was a ship that remained in service at the exact same time the USS Atlantis-E was.
The Atlantis-D was commanded by Captain Nemo. In 2381, it held a very important conference with the Hellonesians. Talks for joining the Federation were canceled when one of the Hellonesian leaders was found dead aboard the ship. An investigation was conducted, but no answers were ever found for the mysterious murder. (Star Trek: Phoenix-X: "The Shadow Maneuvers")