I talked to a Nintendo support representative and asked him if having FE:A registered but not doing the actual registration survey would make me miss out on the $30 promotion. He said he had to talk to his supervisor. The supervisor (Sebastian) said that as long as the game is on your Club Nintendo account the survey shouldn't matter.
So for all you people who bought FE:A while linked to Club Nintendo and forgot to do your survey it looks like you are in the clear! I'm not sure how reliable Nintendo support is because this was the first time I have contacted them. But, it looks like there is hope.
However, if you bought the game Digitally before you registered your 3DS to Club Nintendo than you SHOULD contact support and het them to manually register it to your account after checking your 3DS info.