They must mail in their original return if they have not yet filed one and they can do so now, they don't have to wait on your situation to resolve itself.
Next take a look at your amended return ... did anything change on page 1 in column B ? If not then the amendment changes nothing but the exemption allowance. If the IRS doesn't accept the amended return you will get a letter later which you can respond to ... in the mean time do nothing more.
