Region Lock, XY, ORAS and Pokebank

I'm not 100% sure if this is correct, but I think your PokeBank account is linked to your Nintendo account. So if you could somehow login to both 3DS using your Nintendo account, then it should work well. However, iirc, you can only use your Nintendo account with one 3DS. But like I said, I'm not 100% sure, so don't quote me on this.

Another thing you could try is a system transfer. Basically, you're just going to transfer everything from your old 3DS to your new 3DS. Then again, I'm also not sure about this because they're from different regions.

So in the end, I didn't really help much xD but basically you should just try contacting Nintendo about this

 

Regarding the above post, doing system transfer is impossible with two systems from different regions.
The original question is a bit confusing so I'll just say this: your Pokémon Bank account is tied to your Nintendo ID, so it's stuck on the system it is right now. (unless you do system transfer but that's only possible for another system from the same region)
You won't be able to use Bank to transfer pkmn between games from different regions. What you CAN do, is trade with yourself over wireless connection. XY and ORAS can trade with each other: so use XY on one system, ORAS on the other system, and trade over the pkmn you wanted to carry on from XY to ORAS. It's a bit messier maybe, but I'm pretty sure it's your only way to do this.