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I have a legit shiny rayquaza That was shiny restarted and was a gift from a freind. it was transferred multiple times without a problem through the generations. But now in poke transporter it says my rayquaza is a problematic Pokemon and I can't figure out why. It was legitimately trained to lvl 100, its move set is completely legit yet Pokemon transporter say its problematic, my event genesect that was obtained from me pre ordering white 2 transfered With no problem at all. also my AR salamence was transfred to gen 6 with no problem at all, although it wasn't shiny its IVS were perfect. If you can tell me any way to fix this problem or tell me another way to transfer it to Oras please do.

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Do you have 2 3DS's?
Are you suggesting trading it to y or oras because that won't work the rayquaza is on white 2
Oh, sorry, I didn't read the question right.
here is the problem with a lot of these answers i've been given 1. gts communication is not possible on white 2 and black 2 anymore so that will not work. 2. the rayquaza is on a white 2 copy so it can't be migrated anymore because poke transporter says that my shiny rayquaza is a problematic and refuses to put it in the bank and all communications are not possible in 5th gen anymore

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Migrate> Poke Transporter> Pokémon Bank> PKMN Y/ ORAS

Basically, there's no other way.

If you wish to transfer your Rayquaza from whichever game you have you must do it that order.

Migrating

Gen 3 ( Ruby, Sapphire, Emerald) to Gen 4 (Pearl, Diamond, Platinum)

Poke Transporter

Gen 4 to Gen 5 (Black, White, White 2, Black 2)

Pokémon Bank

Poke Transporter to Pokémon Bank to Y or ORAS

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i did that of course it was transfered through all the generations after hoenn but gen 6 because its "problematic"
Well you could transfer hacked Pokemon up until gen 6 so it could be hacked. My guess would be to check its details and then reconsider whether it has been hacked or not. My guess is that it was obtained by action replay or it was made by Pokegen and the SID was inputted incorrectly etc. Check the details of when and who caught it. Also check its stats, if it has good stats and a good nature, it likely was hacked as the chance of getting a Rayquaza, shiny with the perfect nature and 6IVs is pretty unlikely.
it wasn't hacked I got it from a friend by him shiny restarting many,many,many times and caught it with a master ball on emerald also idk if it has perfect nature but it is shiny, its IVS are perfect but i don't think quirky is the best nature for it, because of what i heard modest was a really good nature for it.
If it is "problematic" however, that alone suggest hacking.
Iv'e heard that Pokebank has such a good hack check that sometimes it thinks legit Pokemon are hacked