Actually I think calling might not be a bad idea ... BUT that can be frustrating anyway, given the call volumes and the fact that sometimes you get someone in a call-center that might not completely understand anyway.
DO the amended return, and yes WITH a copy of the 982 that completely matches up in amounts (AS A PART OF THAT AMENDED RETURN) and send in the cover letter that explains AS WELL.
Whatever you do - Keep a full copy
Then send by private delivery service, such as FedEx, so that you'll ALSO have documentation that it was received.
Here's a site that gives you the addresses to send to.http://www.irs.gov/uac/Submission-Processing-Center-Street-Addresses-for-Private-Delivery-Service-(PDS)
Make sure that everything in that package connects
(copy of the notice, corrected return, corrected 982, letter explaining), so that when they read the notice , they'll see everything there that addresses the entire issue.
Once you have your proof of delivery, through the FedEx tracking number,... THEN you might try calling them to verify, tell them that they have it... even give them the tracking number.
But the main point is that you give them that amended return that covers everything. If you'll spend the 12 bucks of so to send it FedEx, they can't say they didn't receive it.