This error occurs when attempting to perform an action on Pretendo that requires ECommerce servers. The fix for this error depends on what you are trying to do.
To update or install games from the 3DS, you will need to switch back to Nintendo Network via Nimbus to access the eShop. For legal reasons, Pretendo cannot and will not re-distribute this content
Pretendo Network ID deletion currently does not work on 3DS, due to it attempting to access non-existent ECommerce servers.
To unlink a PNID from a 3DS, see Unlinking a PNID. If you wish to delete the entire account, the account can either be deleted through a Wii U, or by requesting it on the Pretendo forums. To do so, log into the account you wish to delete and make a post asking for account deletion. Note that the username will become permanently unavailable upon deletion.