PokéBase - Pokémon Q&A
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So, I know it has been asked many times, but I need to ask out of paranoia hahaha. okay, so I pretty much started playing Pokemon alpha sapphire about a week ago, and I had never played an original Pokemon game before (always used roms, but I always wanted to play the actual game) and while I was playing I used the wonder trading and got a shiny ralts, I played with it basically through the entire game and beat the elite four with it in my team, after checking the IVs, I found that it had perfect IVs and researched a bit and discovered that it could be and most certainly was a hacked Pokemon (it could get into my bank and do free battles in battlespot and etc, but still hacked. no one would trade such a thing in WT, at least I dont think so), in my research I discovered that some hacked Pokemon are indistinguishable from real ones, I tried to keep it as a trophy and never really use it but I just couldn't take it, I was extremely bothered by having a hacked Pokemon in my pc, so I got rid of it and traded it away for someone who doesn't care about "legal" hacked Pokemon. but now I'm afraid because the shiny gardevoir is recorded in my first game clear and hall of fame and it stayed a pretty long time in my game, does this mess with anything or can I consider myself 100% legit again? I mean, the hall of fame record doesn't store Pokemon data such as IVs and stuff right? so I can pretend to myself that it was a normal Pokemon that I traded away hahaha. anyway, sorry for the long post and thanks for the attention, I appreciate it :)) please dont be mean, I just need to let the paranoia away hehe don't judge me for being a Pokemon legitimacy purist :P

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No, it won't mess up your saved file at all.
If the game recognises the Pokemon as being possible to obtain, along with a correct location of obtaining (like tapu koko on route 16 is not possible, yungoos on route 2 is possible), everything is fine. It is recognised as legitimate.
Only Pokemon recognised as legitimate are allowed to be traded.
You shouldn't have traded it away, it was perfectly fine. Also, there is the slightest possibility it was legitimate.

Source: my friend has a similar perfect rayquaza, and has been fine for over an year without trading it away.

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Thanks for the answer man. I actually feel much better after trading it. i got a pokemon that i really wanted in return, so i have no regrets :))
No probs man! Though it could have been legitimate... should've given it to me.