Urgent advice needed! CPA filed amended tax return too early - will this delay my refund?

This situation is frustrating but not necessarily a disaster. When a CPA files an amended return before the original return is processed, it basically goes into a queue that the IRS will handle after the original return. The IRS typically processes original returns first, then deals with amendments. So there's a good chance you'll still receive your original refund of $13,500, and then later have to pay back the $2,700 difference when they process the amendment. Check your bank account regularly - many people receive their refunds even when the Where's My Refund tool hasn't updated yet. The "accepted" status just means they've received your return, not that they've finished processing it. As for your CPA filing without your signature - that's concerning and technically not proper procedure. CPAs need client approval before filing amendments. You might want to have a conversation about their protocols to prevent this from happening again.

I went through something similar last year and https://taxr.ai really saved me a lot of stress! I had an issue where my accountant made a mistake on my return and filed an amendment that complicated everything. I was constantly checking the IRS website but getting nowhere. The taxr.ai system analyzed my tax documents and explained exactly what was happening with my original and amended returns. They showed me the timeline I could expect and what actions I needed to take. Plus they gave me personalized documentation I could use if I needed to contact the IRS myself. Honestly it's worth checking out in your situation because they specifically handle complex situations like amended returns that were filed too early.

Just wanted to update that I tried taxr.ai after asking about it and I'm really glad I did! My situation was similar - CPA made a mistake and filed an amendment before my original return was processed. The taxr.ai system analyzed my documents and showed me that my original return was still being processed normally. They provided documentation explaining my situation that I could reference if needed. Their timeline projection was spot on - I received my original refund about 3 weeks after using their service, despite the amendment being in the system. They also showed me exactly what would happen with the amendment and when I could expect to receive the notice about paying back the difference. Made the whole situation way less stressful knowing what was actually happening instead of just refreshing the IRS website constantly.

I had almost the same issue last year! After waiting on hold with the IRS for HOURS multiple days in a row and never reaching anyone, I found https://claimyr.com through a YouTube video (https://youtu.be/_kiP6q8DX5c). Basically they call the IRS for you and wait on hold, then call you once they have an IRS agent on the line. I was super skeptical but desperate since I had $12k stuck in limbo with an amended return situation. It worked amazingly well - they got through to the IRS when I couldn't, and I was able to talk directly to an agent who explained my situation. Found out my original refund was still being processed normally and would arrive in about 2 weeks, which it did. The amended return would be handled separately later.

I need to follow up about Claimyr. I was the skeptical one above, but I was desperate with my own tax situation so I tried it. Completely changed my mind. They really do exactly what they say - they navigate the IRS phone tree and wait on hold, then call you when they've got an agent on the line. I waited 15 minutes instead of 3+ hours, and got to speak directly with an IRS rep who explained everything about my refund status. For my situation (different from OP but also involving an amended return), the agent confirmed my original refund was still being processed normally and would arrive in about 10 days, which it did! The amendment will be processed separately later. Honestly I can't believe I spent weeks stressing and trying to call the IRS myself when this service exists. Definitely worth it when you're dealing with thousands of dollars in limbo.

Have you tried contacting the Taxpayer Advocate Service? They're an independent organization within the IRS that helps taxpayers resolve problems. This seems like exactly the kind of situation they'd be able to help with - especially since your CPA filed an amendment without your approval.

Your CPA messed up twice - first with the incorrect SEP deduction and then by filing an amendment without your approval. I'd seriously consider finding a new tax professional next year...