"On the 1099-R, the company listed my distribution as a single number, RMD + Conversion which is probably the correct procedure."
I see. You meant that the Form 1099-R does not separate out the conversions, which is as it should be. However, when entering this Form 1099-R you must indicate that you moved the money to another retirement account, that you did a combination of rolling over, converting and cashing out, and indicate the amount converted so that the conversion appears on Part II of Form 8606 and the taxable amount from Part II is included on From 1040 line 4b. It seems that you have done this. If the estimated tax payments were necessary to satisfy your 2024 tax liability, it seems that there was no reason for the IRS to send the funds back to you.
