ive tried the exact same technique and it no longer works on Pokémon crystal on 3ds. All it does is either actually changes the box or it keeps the box but it only has 1 Pokémon with the item in there.
If this glitch is done on the Virtual Console, and then the player uses Poké Transporter, the game will transfer Pokémon from the box the player swapped to, but the Pokémon will remain in the Virtual Console, essentially cloning them again. However, this will glitch Box 1 and make it unusable. Depositing Pokémon inside will disappear, and PokéTransporter will detect the box as empty. Moving a Pokémon into Box 1 will change its nickname to its OT (but without the first character), and delete the OT.
source