Space on your SD card is not unlimited . I suggest you delete a downloaded content that you don't need ,maybe ? If not you can always grab a few SD card for 3DS/XL.
You can buy SD cards on sites like The Official Nintendo Store as well as eBay,Amazon and Argos.
SD cards in the Official Nintendo Store here
All compatiable SD cards are :
Yes you are probably wincing at this word, but you have to pay for Pokemon Bank.
This fee is ¥500 in Japan, $4.99 in the United States and Canada,
£4.49 in the United Kingdom, €4.99 in Europe, $6.50 in Australia,
$8.50 in New Zealand, ₩5000 in South Korea, $150 in Taiwan, $40 in
Hong Kong and R$ 8.99 in Brazil.
If nothing works the only thing you can do is probably contact Nintendo.
Or you can go on their Tech Help Forums