The captain, Francesco Schettino, has been charged with manslaughter and dereliction of duty. His lawyer, Domenico Pepe, said changes to the bridge command center might have been made by "people who had no interest in clarifying things," the Italian news agency ANSA reported.
Pepe said there is no way now of determining how the bridge command center was arranged at the time the vessel hit a rock of the island of Giglio.
The vessel had been sitting on its side, semi-submerged until it was brought to the surface last summer.
Three judges, accompanied by court-appointed experts and lawyers for Costa Cruises inspected the ship Thursday. They were the first party to board the Costa Concordia since it was righted.
Prosecutors say Schettino altered course to go close to the island of Giglio because he wanted to signal a friend. The disaster killed 32 people.