Either approach should work but I'd probably opt for amending and - probably - getting a small refund for your effort. You can now e-file amended returns and I'd think that would put the problem to bed, but a belt and suspenders approach, (always a good idea when dealing with the IRS), would be to also mail a paper copy of the amended income tax return, along with a brief note of what happened, to where ever the letter from the IRS directs you to respond.
I would guess that since the law was changed to brokers only indicating your "out of pocket" cost of the stock instead of the correct basis on the 1099-B, the IRS has sent out hundreds of thousands of these "your 1099-B is missing" letters.
