Why would that matter? If I had an 8" AR pistol in .556 that shipped from the manufacturer with a brace, then I sold the 8" upper, and I swapped on a .300 Blackout upper, with a 16" barrel, would it be in violation of the new rule? How is a brace different from a stock, grip, muzzle device, bump stock, or magazine? It is an accessory, not the gun, so why can't it be removed, or swapped out for a "legal" brace?
Here is what is going on. Now don't expect it to make any sense, since it is the ATF we are dealing with.
If you purchased a braced "pistol", and it won't pass the new scoring sheet, then the ATF will consider that it shipped from the factory as a rifle, specifically an SBR. A lower/receiver that began life as a rifle cannot become a pistol. However, if you purchased it without the brace, or built it without the brace, then it began life as a pistol. You added a brace to it later, and if that configuration doesn't pass the new scoring sheet, then you made an SBR. However, in this case, since it started life as a pistol, you can remove the brace and it magically becomes a pistol again.
So, a pistol can become a rifle and back to a pistol (and back and forth ad infinitem) with the ATF's blessing.
Your original pistol, if it shipped without a brace, will be just fine if you ditch the brace. If it meets the scoring sheet with your brace, then you will also be good to go.
A rifle can never become a pistol, it can only become an SBR with a barrel shorter than 16". If the braced "pistol" that you purchased is actually considered now by the ATF to be a rifle (even if unknown to you at the time of purchase), then you have four options:
1) Put a rifle length barrel on it, with or without the brace or a stock.
2) Pay the $200 tax for your new SBR, with or without a brace or a stock.
3) Destroy the firearm portion (for an AR the lower rkeceiver).
4) Risk going to prison for a long time for possession of an untaxed SBR.
Now, in the case that you described, you met option #1 by installing a legal rifle barrel. You do not, HOWEVER, need to destroy or get rid of your short upper. You can get a pistol lower and install it without a brace, or in a braced configuration that meets the new scoring sheet criteria.
Like I said, don't expect any of this to make any sense, just like the rest of the NFA.