I just bought Omega Ruby and wanted to transfer my pokemon from Y to it so I used some extra cash on the eshop to buy the Pokémon Bank. I got the pokédex because you can't transfer to the game without it, saved, and transfered my pokémon, including A LOT of legendairies and a few fully EV trained ones, as well as some with Pokérus. I started up Ruby and to my horror, they were all gone. Nothing in the boxes, my game also somehow reverted back to a save BEFORE I had my pokédex. I got it back, checked the pc again, and nothing is there.
I hope there is some way possible to restore it. If it's all completely gone, I won't want to play Ruby, I'll probably just take back. Will bother me too much that I just lost months of effort and time to build up my team.
-Raztaztic.