You simply write a letter to BATFE with the serial number of the registered gun, explaining that you have replaced the short barrel with a long one, and requesting that the rifle be removed from the NFRTR. They will reply either that that has been done or advise you if there is anything else you need to do.
But I am a bit confused. You have a 9" barrel upper, and you have a lower that it fits, so you already have an SBR and it is not registered. You should have obtained Form 1 approval before buying the upper. I hope I am wrong, but it looks like you have already violated the law.