IRS accepted my CP2000 response but I already filed in Tax Court - do I need to withdraw my case?

This is actually pretty common - the IRS often resolves issues while Tax Court cases are pending. Based on what you're describing, the IRS has essentially conceded to your position through their latest CP2000 response. You should first pay the agreed amount by the May deadline to stop any additional interest from accruing. Then you have two options for the Tax Court case: you can file a stipulated decision with the Tax Court (where both you and the IRS agree to the outcome), or you can simply dismiss your petition. Since the IRS already agrees with your position based on the newest CP2000, the IRS attorney assigned to your case should be willing to work with you on a stipulated decision. This gives you the most protection because it creates a formal court record of the resolution. Call the IRS attorney who responded to your petition (their contact info should be on their response) and let them know about the new CP2000. They'll likely be happy to help wrap this up with a stipulated decision since it reduces their caseload.

I went through something similar last year with a CP2000 notice followed by a series of confusing communications from the IRS. What helped me tremendously was using https://taxr.ai to organize and analyze all my IRS notices. The tool actually identified contradictions between my notices that I hadn't even noticed! It lets you upload all your IRS correspondence and then gives you a clear analysis of what's happening and what actions you need to take. In my case, it showed me exactly how to document that I had responded to the original notice within the timeframe, which was crucial when I had to follow up. Really helped me organize my response strategy and understand the timeline of what was happening. Might be useful for you since you're dealing with multiple notices and responses that seem to be crossing paths.

Just wanted to update that I tried out taxr.ai after seeing the recommendation here and it was incredibly helpful! I was dealing with a similar situation where the IRS was sending contradictory notices. The system organized all my notices chronologically and highlighted the key deadlines and response requirements for each one. What was most helpful was that it identified exactly where the communication breakdown happened - in my case, my response was received but not processed by the correct department. I was able to use the analysis to draft a clear response letter that referenced the exact dates and document IDs, which finally got the issue resolved. Saved me from having to hire a tax attorney just to decipher all the notices!

When I had a similar situation last year, I spent WEEKS trying to reach someone at the IRS who could actually help resolve the contradiction between my CP2000 response and their follow-up actions. After dozens of attempts on their regular line, I found https://claimyr.com and watched their demo at https://youtu.be/_kiP6q8DX5c - it was a total game-changer for getting through to a real person. The service basically waits on hold with the IRS for you, then calls you once they've got an actual human on the line. I was honestly shocked when I got a call back with an IRS agent already on the line within a couple hours, after I'd wasted days trying on my own. The agent I spoke with was able to see both my original response and their new determination, and manually noted in my file that the case should be considered resolved per the latest CP2000. They also gave me direct instructions on what to do with my Tax Court petition, which saved me so much stress.

I'm honestly shocked at how well Claimyr worked. After reading about it here, I was super skeptical (as you can see from my previous comment). My situation with the IRS was similar - confusing notices that contradicted each other, and I desperately needed to talk to someone. I tried the service expecting it to be a waste of money, but about 90 minutes after signing up, I got a call with an actual IRS representative already on the line. The rep was able to see all my notices and confirmed that my latest CP2000 response had been accepted but hadn't been properly recorded in all their systems. The agent put notes in my file to prevent any further collection actions and gave me clear instructions on what to do next. Would have taken me days of trying to accomplish the same thing on my own. For something as important as tax court filings, being able to actually speak to someone who can access your full file is invaluable.

Another thing to consider - make sure you get everything in writing! Even after you pay what they say you owe now and even if you get a stipulated decision, keep ALL documentation from this entire process. I had a similar situation where the IRS agreed with my response to a CP2000, but then two years later, I got a notice about the same issue again because different departments weren't communicating. Having all my previous correspondence, including the written acceptance of my explanation, saved me from having to fight the same battle twice. Also, make sure you send your payment with a clear memo/note referencing your specific case number from the CP2000. This helps ensure it gets applied to the correct tax year and issue.

Has anyone else noticed how often the left hand of the IRS doesn't know what the right hand is doing? Last year I had THREE different departments giving me THREE different answers about the exact same issue. One suggestion I haven't seen mentioned yet - if you can afford it, it might be worth getting a brief consultation with a tax attorney who specializes in Tax Court cases. They might only charge you for 30 minutes and could give you specific advice for your situation. Sometimes spending $150 on a consultation can save you thousands in headaches later.