I had an issue related to my divorce in 2014 where they tossed out my return because they didn't believe it. I was due quite a bit in a refund. In resolving it, I made at least 10 phone calls to the IRS, each time they saw the notes, and said they would get back to me - sometimes wanting me to send in a copy tax return again, etc. The last time - 2-1/2 years later - which was quite funny, the lady that took my call, said she needed to check it out, thought she put me on hold, but I got to hear her conversation with another IRS agent, I think he was from Buffalo. He thought I was wrong in my filing, but recommended the following:
They referred me to this IRS Tax Advocacy group, which is totally separate, he looked at my return, and said yes, it it quite clear you are due this refund, and it was all resolved. So it takes patience to make it work, but there is a 3 year deadline on getting things resolved, as I was up against that with mine.