Many may know the incident when I traded my legit Rayquaza for a hacked Pokemon without knowing, then tried to get it back... But now, I knew I still had the rayquaza ever since. I played with it non-stop ever since the trade happened. Rayquaza reached level 100. But then I stopped playing for months, because X came out. I came back to find Rayquaza is missing. I checked the day care and did pokesearch in the boxes, but never found it! I also found my shiny mew, celebi, and mewtwo are missing! So basically, my question is how did these Pokemon go missing? Was there a memory issue? Corrupted data?
Edit: I stopped using Dream World Before B2 and W 2 came out, so it couldn't be that
It is probably because you haven't played the game for months because the game will mess up if you don't play it. I was grounded from my ds for two months and when I got it back, it wouldn't work but when it worked, I lost all my Pokemon in my PC Box. The hacked shiny mew you got could've also messed up your game since you traded your rayquaza then got it back but this happens from time to time with lots of games and it is a possibility some of your data was corrupted since you haven't played it.