Once you have the transcript, look for evidence that an amended return was filed and a revised tax assessed. I bet it won't show up on the transcript at all.
Your next choice is based on whether or not the amendment was received and a revised tax assessment made. If so, the transcript would then show any administrative action taken to reject the filing.
If the amendment does not show up, if you can prove you filed it, now decide if you want to pursue this. You should be able to do it yourself.
You could go to Appeals and argue your claim, but if no amended return shows up, they could argue they have no jurisdiction.
The last place I would try is the taxpayer Advocate office, or TAO. Completing and filing form
911 will get an advocate looking into your case.
I have had great results with Advocates; they are among the Service's best and most knowledgeable people. Their mandate is to look into things, and process cases quickly and keep taxpayers informed.
I hope this gives you some insight and options about what to do next. Thanks from Just Answer/Pearl. Please ask follow up questions, or leave positive feedback to close out your question.