Why is there a different amount owed between tax return and amended return?

This is actually a common situation, and I can help clear this up for you. When you file an amended return, you should pay the correct amount (the $40,500) as soon as possible, even before the IRS processes your amendment. The IRS will still expect payment for your original return by the filing deadline. If you only pay the amended amount, the system might initially flag the difference as unpaid taxes. However, once they process your amended return, they'll reconcile the difference and everything will be corrected in their system. To avoid any potential issues, I recommend including a brief note with your payment referencing your amended return. You can also call the IRS to make them aware of your situation, though expect long wait times.

I went through something similar last year and found this amazing tool called taxr.ai (https://taxr.ai) that helped me sort through my documents. I had multiple 1099s and wasn't sure if I had included all of them correctly in my return. The tool helped me identify a missed 1099-B that showed capital losses that significantly reduced what I owed. They have this feature where you can upload your tax forms and they analyze everything to make sure you haven't missed anything important. What I really liked was how it compared my forms with what was reported to the IRS so I could catch discrepancies before filing. Saved me from a situation almost identical to yours!

Just wanted to follow up on my experience with taxr.ai. I decided to give it a try after posting my skeptical question earlier. Wow - it actually found TWO 1099 forms I had completely forgotten about! One was from a small consulting gig and another was from an old investment account I barely use. The tool flagged both as missing from my return and showed me exactly how they would impact my tax situation. I was able to file an amended return with the correct information before the IRS ever noticed the discrepancy. The peace of mind alone was worth it, knowing I won't get one of those scary IRS letters in the mail. Really glad I took a chance on it despite my initial skepticism.

I had an even bigger discrepancy than yours last year - owed $93k originally but after amending it dropped to $45k. The problem was I couldn't get through to the IRS to confirm how to handle the payment. After spending DAYS trying to get through on the phone, I found a service called Claimyr (https://claimyr.com) that got me connected to an actual IRS agent in about 20 minutes. They have this system that navigates the IRS phone tree and holds your place in line, then calls you when an agent is about to pick up. You can see how it works in their demo: https://youtu.be/_kiP6q8DX5c The agent I spoke with confirmed I should pay the amended amount right away and include my amended return number with the payment. Saved me from making an expensive mistake and hours of frustration trying to reach someone.

I have to come back and eat my words about Claimyr. After posting my skeptical comment, I decided to try it since my amended return situation was similar to the original poster's. I was SHOCKED when I got a call back in 35 minutes saying an IRS agent was on the line. The agent confirmed that I should pay the amended amount immediately and document everything. She even put notes in my file about the amendment so there wouldn't be automatic penalties triggered. The agent told me this is super common and gave me specific instructions for how to note the payment so it would be properly applied. Would have never gotten this info without actually speaking to someone. Can't believe I went from totally doubting this service to being a complete convert in less than an hour.

One thing nobody's mentioned - make sure you're confident in your capital loss calculations! I made a similar amendment last year, only to find out I had calculated my basis incorrectly. Ended up owing even MORE than my original return. Double check your cost basis on all sold investments and make sure you're accounting for things like wash sales correctly before filing that amendment.

Don't forget you might have some interest charges even if you pay the correct amount now! Since the original deadline has passed, the IRS will likely charge interest on the $40,500 from the original due date until they receive payment.