u/promdog

Long post but I want to give full context because this situation has been a saga.

Background

I've been with the same tax prep firm for nearly 10 years. They're primarily a business-oriented firm that has kept me on as a personal filer out of loyalty. This year my return was handled by someone I've never worked with before.

The OBBBA Overtime Deduction

My original 2025 return was filed and signed in mid-March. A week later I discovered, through a family member in accounting, that the One Big Beautiful Bill Act introduced a deduction for the FLSA premium portion of overtime pay for 2025-2028. I had a meaningful amount of overtime on my W2. The deductible premium portion is approximately 1/3 of total overtime, worth a few hundred dollars in federal savings.

My tax preparer never asked about overtime. Never mentioned the OBBBA in their planning opportunities summary. I had to bring it to them myself.

The Documentation Battle

My preparer initially said they needed a formal employer breakout of the FLSA premium portion, not just my pay stub. I went back to my employer's payroll department, who called their payroll provider directly. The response was that there was "no qualified OT to report for 2025" because the reporting infrastructure wasn't in place yet.

I then found IRS Notice 2025-69, which explicitly states that when an employer cannot provide a separate accounting, the employee may use pay statements and apply a reasonable method to calculate the premium. I sent this to my preparer and they finally agreed to proceed using my pay stub.

The Amendment

The amended return was signed April 1, well before the April 15 deadline. My preparer filed a 1040-X. On April 15, three payments hit my checking account exceeding my amended balance due by roughly $800. Two payments were labeled "Amended Return Payment" for the same amount, and a third was labeled "Balance Payment." The duplicate is clear.

My Questions

After researching, I came across guidance indicating that when a correction is caught before the filing deadline, the correct approach is to file a superseding 1040, not a 1040-X. A superseding return replaces the original entirely and is treated as the controlling document. A 1040-X filed before the deadline can create confusion and processing delays.

My preparer pushed back on this, saying superseding returns are "edge case" and the 1040-X was appropriate, and that the duplicate payment was an IRS processing issue unrelated to the form type used.

The IRS transcripts show the overpayment is on record but the amendment has not fully processed yet. I'm being told to wait and keep calling the IRS myself, which so far has meant two hours on hold ending in a disconnection.

1. Was a superseding 1040 the correct approach given the amendment was filed before the deadline?
2. Could the 1040-X filing method have contributed to the duplicate payment?
3. Is my preparer responsible for resolving this, or is this truly on me to chase with the IRS?
4. The IRS website states amended returns take up to 16 weeks to process. Does that apply to overpayment refunds as well, even when the overpayment is already showing on the transcript?

Thanks in advance.

Long post but I want to give full context because this situation has been a saga.

Background

I've been with the same tax prep firm for nearly 10 years. They're primarily a business-oriented firm that has kept me on as a personal filer out of loyalty. This year my return was handled by someone I've never worked with before.

The OBBBA Overtime Deduction

My original 2025 return was filed and signed in mid-March. A week later I discovered, through a family member in accounting, that the One Big Beautiful Bill Act introduced a deduction for the FLSA premium portion of overtime pay for 2025-2028. I had a meaningful amount of overtime on my W2. The deductible premium portion is approximately 1/3 of total overtime, worth a few hundred dollars in federal savings.

My tax preparer never asked about overtime. Never mentioned the OBBBA in their planning opportunities summary. I had to bring it to them myself.

The Documentation Battle

My preparer initially said they needed a formal employer breakout of the FLSA premium portion, not just my pay stub. I went back to my employer's payroll department, who called their payroll provider directly. The response was that there was "no qualified OT to report for 2025" because the reporting infrastructure wasn't in place yet.

I then found IRS Notice 2025-69, which explicitly states that when an employer cannot provide a separate accounting, the employee may use pay statements and apply a reasonable method to calculate the premium. I sent this to my preparer and they finally agreed to proceed using my pay stub.

The Amendment

The amended return was signed April 1, well before the April 15 deadline. My preparer filed a 1040-X. On April 15, three payments hit my checking account exceeding my amended balance due by roughly $800. Two payments were labeled "Amended Return Payment" for the same amount, and a third was labeled "Balance Payment." The duplicate is clear.

My Questions

After researching, I came across guidance indicating that when a correction is caught before the filing deadline, the correct approach is to file a superseding 1040, not a 1040-X. A superseding return replaces the original entirely and is treated as the controlling document. A 1040-X filed before the deadline can create confusion and processing delays.

My preparer pushed back on this, saying superseding returns are "edge case" and the 1040-X was appropriate, and that the duplicate payment was an IRS processing issue unrelated to the form type used.

The IRS transcripts show the overpayment is on record but the amendment has not fully processed yet. I'm being told to wait and keep calling the IRS myself, which so far has meant two hours on hold ending in a disconnection.

1. Was a superseding 1040 the correct approach given the amendment was filed before the deadline?
2. Could the 1040-X filing method have contributed to the duplicate payment?
3. Is my preparer responsible for resolving this, or is this truly on me to chase with the IRS?
4. The IRS website states amended returns take up to 16 weeks to process. Does that apply to overpayment refunds as well, even when the overpayment is already showing on the transcript?

Thanks in advance.