I just got this same error with a 2DS.
I've used my flash card to install via ntr boot, boot9strap to many consoles. It's just this 2DS that no matter what, won't boot boot.firm, and the console will just turn on as normally expected (it's not bricked as OP's).
Guess it's a button problem? Although the 2DS is brand new and START, SELECT and X seem to be working alright. Anyway, just tested the card on another 2DS after this, and it worked no problem.