I am very new to this all, I have not owned anything Nintendo since the original Wii launch. I recently picked up a used 3DS which has 2 games on it I would like to keep. It still has the previous owner's Nintendo ID and settings on everything. I am wondering if I can use a new Nintendo ID (I want to be able to make my own purchases in the store) and still keep the downloaded games? Are they stored on the SD card or system? Would also like to know if there's a way to bring a 3ds completely back to default and keep the downloaded games.
The short answer is
All games you digitally purchase from the Nintendo eShop are tied to the Nintendo ID used for purchase. As soon as you change the Nintendo ID in your 3DS/3DS-XL, the old games become inaccessible. The only way you can regain access to them through your Nintendo ID would be to purchase them from eShop using your Nintendo account.