Recently I've linked my 3DS to my Nintendo account and found out that digital games (bought through the eshop) will only link if bought after the 3DS is linked with the account.
I bought the game before I linked my 3DS - if I delete the game and re-install it (now that I have linked my 3DS with my Nintendo account) will it also link with my account?
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I don't think so, to be honest. Some of the digital stuff on the 3DS and Wii is utter rubbish, Nintendo can't make online systems very well.
I don't think it will link, but you might be able to redownload the game. I wouldn't try though, you might lose it. There's an FAQ here:
Game
Why not use flashcart?
Once you use the R4i gold 3ds card, you will never have such questions,
You could download any games you like into a SD card.
And play them at any NDS or GBA console.