By law, the initial making of an NFA item should match the Form 1.

If you have an approved Form 1 but have not yet made the NFA firearm, yes, you can send them a letter stating that after receipt of the approved Form 1 and prior to the initial making of it, you discovered that you needed to make it with a different barrel and OA length as specified, and asking them to amend the NFA Registry to reflect the actual dimensions, you should be OK.

Just send the letter in duplicate with a photocopy of your Form 1, include an SSAE, and ask that they mark one copy as "received" and return it to you in the SSAE. Once you have the returned copy of your letter in-hand, proceed with the "making" to the new spex.

HTH.