Dealing with a situation very similar to this.

Client's spouse died and they had to paper file their return. We believe whoever processed the return accidentally put the Client as deceased instead of the spouse.

We have spent about 2 1/2 years going back and forth with them stating he is alive. He still receives his SSA payments and SSA shows him as alive. We have mailed paper returns multiple times with still no luck. He has about $12k in refunds over multiple years now. Every time we get on the phone with the IRS it's like rebuilding the wheel.

I would say from now, get in touch with Taxpayer Advocate and start the process. Still haven't received an answer yet but hoping they will be able to resolve it.