We received a CP2000 notice for 2020 tax year in May 2022. I checked that I did not agree with the notice and send back a letter explaining my reason. I had forgot to report my 1099 short and long term gains though we reported my wifes accurately, they were assessing the gains/tax for both of us as though neither were reported. My accountant told me to submit an amended return which I did in September 2022. He said this would clear things up. In the mean time I received a CP3219A notice of deficiency which said to appeal to tax court by May 10, 2023. I checked the 'where's my amended return' IRS website last week and it stated that there was an adjustment though it does not say completed. And my online transcript still shows values from original return.
My question is, is it too late to send appeal to tax court since it would be a month late? I'm not sure if my tax accountant is correct about this, he said to just wait for the amended return to be processed, that they have to process it and if they disagree with it they have to tell me what they disagree with. He said that the clock for tax court is reset with the adjustment letter that will be sent to us? I'm positive the IRS made a mistake on their assessment though I'm not sure if I'm now stuck paying what they calculated?
