After you file

I'm not sure exactly what I'm supposed to do at this point. Anyone have any suggestions?

 

Respond in writing that you dispute and you intend to amend.

 

Prepare Form 1040-X with Schedule D and Form 8949.

Do not include your old 1040 nor your revised 1040 because the Form 1040-X reflects any changes there and becomes your new tax return.

 

Send to the address in the Form 1040-X Instructions,

or, to the address in your letter if it says to do that.