The fact that it may not be possible to prove that you knowingly & intentionally possesed a SBR prior to having an approved stamp does not negate the fact that constructive or physical possession of said item before hand is still illegal. Yes, it's tough for a federal agency such as the BATF&E to keep tabs on every AR owner that may have an unauthorized item in their possession, however, now you know & I personally wouldn't want to take the chance. Get your stamp first & then buy as many uppers that you want for each registered lower you own.
As far as an M16 writing a letter to the BATF&E to advise of an upper change, is that possible? Are you asking does the owner have to write them to advise? I think you are supposed to, but I've never heard of it being a problem if you don't. Just follow the instructions on the Form 1 & you will be ok as long as the new or swapped barrel length is in excess of what you already have registered. If you want to go shorter than what you have registered then you have to pay another $200 on another lower IIRC & list the shorter lenght.
I've never listed OAL & have always listed barrel length at 7" as well. All of us at work have done this & the forms were approved in less than 30 days accompanied with a dept. letterhead advising our intent & request for expedited processing. No Form 1's have been returned for clarification or correction in the process either.
"People sleep peaceably in their beds at night only because rough men stand ready to do violence on their behalf." --George Orwell--
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