You can only wish for one at a time. The next time you come back (24 hours later), you will have to find the ones you want again.
After exploring an area, players will go to the Tree of Dreams, where they may choose to leave a Berry in the tree and make a wish to choose one of their befriended Pokémon to send to the Entralink. If they do, they may not revisit the Island of Dreams until the next trip. However, if they do not choose to make a wish and befriend a Pokémon, they have the choice of visiting the island again to look for more Pokémon and items. Upon entering the Island of Dreams a certain number of times, players will start to find nothing on the island. If there are fifty Pokémon ready to be taken back to the game, the Island cannot be visited. In the Japanese version there originally was a maximum limit of 50 Pokémon to be transferred at all; however,
this was removed in 2010.
~Bulbapedia
