I had collected all of the pokemon necessary for the shiny charm in my Y game and saved them in Pokebank. I know exactly what was stored there and even how some of the boxes were arranged, and some I know general levels. A few even had Pokerus.
I went to transfer my Pokemon to Alpha Sapphire today to get the complete the dex in my new game, and I noticed about 50 were missing. I have absolutely no idea what happened. They were all legitimately caught, and were safely transferred. I never tried anything funny like resetting to duplicate them or anything either.
I have checked with the search function in all of my games and the bank and cannot find them.
Has this happened to anyone? What can I do at this rate?
This really makes me mad since these took so long to collect.