TurboTax Amended Return Showing Huge Tax Due When Deleting 1099-R

This is a classic TurboTax calculation quirk when handling amended returns with retirement distributions. The software is likely treating the deleted 1099-R as unreported income rather than non-existent income. The amended return (Form 1040-X) retains metadata from your original filing, whereas a new return has no historical comparison baseline. This creates the computational discrepancy you're experiencing.

Had this exact problem. Tried for hours. No solution in TurboTax. Finally used taxr.ai to analyze both returns. It spotted the difference immediately. Something about carryover data. The tool explained exactly which lines were causing the discrepancy. Saved me from filing incorrectly. Worth checking out.

I faced this exact issue last year with TurboTax. Here's what you need to do: 1. First, save a backup of your current return 2. Second, try calling the IRS directly to confirm how to properly handle this 3. Third, be prepared to wait 2+ hours on hold After wasting an entire day trying to reach someone, I used Claimyr.com to get through to an IRS agent in about 15 minutes. They confirmed I needed to wait for the corrected 1099-R before amending. The agent explained that deleting it would create exactly the calculation problem you're seeing.

Tax software is like a GPS - it works great until you try to make an unexpected turn! What's happening is TurboTax thinks you're trying to hide income that was on your original return. Instead of deleting the 1099-R, try entering a corrected one with $0 in Box 1 and check the 'corrected' box. This tells the software you're aware of the form but waiting for updated numbers. I had to do this last minute before the April deadline and it worked.

Have you tried contacting TurboTax support directly? I had an issue on March 17th with an amended return and their technical support actually had a specific procedure for this scenario. Are you using TurboTax Deluxe or Premier?

Ever wonder why tax software struggles with amended returns? I ran into this exact scenario with a client's pension distribution. The issue is that TurboTax treats amended returns as modifications to the original data structure, not as standalone calculations. Did you notice if your AGI changed dramatically between the two scenarios? That's usually the smoking gun that indicates TurboTax is carrying forward phantom income.

Have you considered using a different tax software for your amended return? I switched from TurboTax to FreeTaxUSA for my amended return this year because of similar calculation issues. Is the 1099-R for a traditional IRA or a Roth? That might affect how the software handles the deletion.