This is what happened in "Deadlock":
Voyager traveled through a dense nebula in an effort to avoid the Vidiians. When the ship left the nebula, a duplicate ship was created. The original Voyager was damaged, but the duplicate was not. The original Naomi Wildman died after her mother Samantha Wildman gave birth to her (for technical reasons). The original Harry Kim fell to his death through a hull breach. The Vidiians detected the duplicate Voyager and boarded it. Janeway of the duplicate ship ordered her Harry Kim to take a healthy and very alive Naomi Wildman to the damaged original Voyager. The Vidiians killed several members of the duplicate Voyager's crew, including Tuvok and Tom Paris. Janeway of the duplicate Voyager destroyed it and the Vidiians, via a self-destruct sequence. The original Voyager remained intact, but damaged by the end of the episode. Among its new crewmembers were the duplicate Harry Kim and Naomi Wildman.
Due to its unusual bio-neural circuitry, Voyager was duplicated on the Demon class, along with its crew. Since the ship was slowly falling apart, as long as it and the crew were away from the Demon planet, the Doctor was not salvageable, since it was part of the ship's systems in the first place.