Here's a question that I haven't been able to find an answer for online:
I have a copy of Pokemon X which I play on my 3DS and a copy of Pokemon Y which I play on my 2DS. I've currently only got Pokemon Bank installed on my 2DS and have only been using it with Y, but I would like to use it with X as well. The game's manual warns against playing the game on a different system to usual as it can interfere with clock-based events or lose your friends list, but is it OK to put use my X cart in my 2DS just to use Bank? Technically, I wouldn't be loading up the game so I'm not sure if it would count as playing it on a different system.
Aside from what the manual says about the in-game clock (I also think your friend's list may get problems too, not sure), I don't think nothing too bad will happen. But usually when a game is played on another system that has wifi features like X/Y, there could be some minor problems.
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Using Pokemon X and Y on a different system shouldn't have any long term effects. It might stop daily events from happening and berry plants from growing until you've saved the game and midnight has passed twice.
@RabidPikachu Pokemon transporter can only transfer Pokemon to a Pokemon Bank box, so you'll need to buy another Pokemon Bank subscription to use it.
you can download pokemon bank on to a different system but it wouldn't be the same pokemon bank that is on the other one unless you transferred your NNID to the different system. I finally got my old Pokemon XL fixed and I have Pokemon Bank on it and on my 2DS but they aren't the same Pokemon Bank because they are tied to two different NNIDs. I gave my Pokemon XL to my son and am keeping the 2DS until they release the smaller New 3DS or announce the AC Happy Home Designer New 3DS XL here in NA.
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Topic: Pokemon Bank question
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