It was in the Anime, when Lugia bred.
A parent Lugia and its child (nicknamed Silver by Oliver) lived near Silver Rock Isle in the Whirl Islands. Dr. Namba attempted to capture both the parent Lugia and Silver for Giovanni in The Mystery is History, A Parent Trapped!. and A Promise is a Promise. Ash and Misty (Brock was not along with them) act as if this was their first time seeing a Lugia, as if the second movie never took place. Meowth, as well, said that he'd "never seen a Pokémon like that before!" On the contrary, the dub pays mention of the Lugia that was seen in the Orange Islands, with both James and Ash stating that it was "like" the one they'd seen in the Orange Islands. In both versions, Ash first refers to the baby Lugia as a "mysterious Pokémon."
Here's a Youtube Video I found.