Amended tax return to change filing status and split taxes paid on original tax return

My wife and I initially filed our 2024 income tax return jointly, but then we amended it to the filing status of “married-filing separately” to reduce our state income taxes. As a result, our total federal tax liability increased by only $3, which my spouse paid with her 2024 Form 1040-X.

 

We paid a large balance due on the original return. On the amended returns, we split that payment between the two of us so that I owed nothing on my return and my wife only owed $3 on her Form 1040-X. But IRS sent me a refund for the amount that my wife claimed and then they will want my wife to pay them back that amount with interest and penalty for late payment.

 

According to Treasury Regulation § 1.6015(b)-1(b), my spouse and I are permitted to split the payments made with our original joint return however we agree. AI Google says, "While Treasury Regulation § 1.6015(b)-1(b) primarily addresses estimated tax payments, the principle that spouses can agree on an allocation generally extends to other payments made with a joint return. Tax code section 6015 was repealed; however, the regulation has continued to guide IRS practice regarding how to divide estimated tax payments." 

 

Our total tax on the two amended returns only increased by $3. So common sense would say that all we needed to do was to pay the extra $3, but I know the law does not always use common sense. So, my question is, am I correct that my wife and I can agree to split our tax paid on the original joint return however we want on our amended separate tax returns, or must I claim the entire amount on my amended tax return and my wife now owes a large amount with interest and penalties?

 

Thank you in advance for your replies.