I electronically filed a 2018 1040 return on 08/30/19 and received an acknowledgement back from Proseries that the return was accepted on 9/03/19 but when the client checked her (spouse) IRS transcript on 1/3/2020 the account shows the return has not been received. She has also received a letter from the IRS stating her return was not received. Her husband (the taxpayer) is not receiving any letters. Is it possible that the IRS only has the return on his account and not hers?
Did you accidently file the return as filing separately? Did you try getting a transcript for him?
"She has also received a letter from the IRS stating her return was not received."
Seems awfully quick for IRS to be sending letters about 2018, or did she file an extension or send them a payment in her SSN only?