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I think that's the issue, the payments should be on line 26.  With electronic payments you don't file a 1040ES per se, no voucher required, making a payment electronically designated as Estimated Tax is a 1040ES.

I don't know enough about any special IRS dealings in this situation, but I am guessing you will end up needing to amend your return to designate your payments as estimated tax instead of withholding and that will presumably bring everything into balance at the IRS.  Sounds like you are correct not to cash the check, presumably the IRS would at some point catch up on the withholding mismatch and then say you underpaid!

The biggest issue with the amendment will probably be the underpayment penalty - when you switch to ES, even tho you paid the full amount of tax, if you didn't pay ES evenly each quarter then likely by default you will see a large underpayment penalty; it's assumed the income/tax is incurred evenly thru the year and the withholding/estimated tax needs to line up with it.  The penalty calculation is done quarterly not annually, so you can be fully paid by year-end or even have a refund, but still have an underpayment for Q1, Q2 etc.  Withholding is treated differently, it's assumed to be 'timely' with the associated income so I think that's why it didn't trigger a penalty before.

If you on TT desktop then in Forms mode you can double-click on the 1040 penalty line and again on the worksheet to bring up Form 2210 with the underpayment calculations. 

For your situation tho, if you paid ES when you did the conversions, you will probably need to adopt the Annualized Income method on Form 2210 to show that the ES lined up with the correct quarterly timing for the income, which will significantly reduce if not eliminate the penalty.  You'll need to provide AGI, Cap gain info thru the year for 3/31, 5/31, 8/31.  This is under Other Tax Situations / Underpayment Penalty.  You may have the same situation with your state tax.

Just a quick example to illustrate, assume no other income and you needed to pay 100k to meet safe harbor, but paid 50k in Q3 and 50k in Q4 for 2 Roth conversions in those quarters.  Without the AI method, then by default the 100k tax needs to be paid 25k per quarter.  So in this situation you would have 25k underpayment from Q1, 25k underpayment from Q2, those underpayments are eliminated in Q3 when the 50k is paid and the penalty stops accruing, but now you are still 25k underpaid in Q3 until the final payment in Q4.  Overpayments earlier in the year will carry forward and eliminate underpayments in later quarters, but no amount of overpayment later in the year will eliminate underpayments in earlier quarters, tho will stop the penalty interest from accruing.

For 2025 if you're planning the same level of conversions but didn't pay ES for Q1 you can take the same approach and pay ES along with the conversions and file AI method again for 2025.  Or figure your quarterly ES payments based on either 100/110% of 2024 or 90% of 2025 tax, tho you may still get some penalty for Q1 if you missed the 4/15 deadline.

You can do the ES calculations under Other Tax Situations / Form W4 and Estimated Taxes and provide 2025 income information to optimize the payments.  If you don't provide 2025 info, TT will generate ES vouchers by default based on 100/110% of your 2024 tax and assumes 2025 withholding is the same as 2024 - so another ramification of your situation is it's possible TT assumed the same large withholding for 2025 and generated ES vouchers much smaller than needed.  Again you don't need these physical vouchers when paying electronically.

Again not a CPA/Expert and not sure all the mechanics of this situation with the IRS, but hope this helps.