Suddenly all 2025 estimated tax payments have gone missing from IRS system

We received a CP23 asking us to pay almost $100K for unpaid 2025 tax plus some interest and penalties yesterday. What it looks like is that they have not credited any of our 2025 estimated tax payments.

What is odd about this, we usually do all payments through my wife's online account and as far as we remember everything looked fine in April when we filed our final return. The final return payment was about $5K, and the math suggests the IRS applied this payment plus a small amount of withholding. But now in May, my wife's account shows no payments for any year prior to 2026, and the 2026 payments now all show pending not accepted and this includes those for TY2025 and TY2026. This is even more odd as things were fine in April, and the IRS has even applied our final payment which now it claims is only pending. So something is very wrong suddenly and that seems to have generated a CP23 as the result. And yes, we can go to our bank account, and all these missing or pending payments have long been removed from our actual bank account, so we have made these payments all on time and in full. It is just that the IRS suddenly claims that they have either not been made at all, or are all pending.

Another thing I worry about this, will the IRS suddenly try to reprocess all these pending transactions. This could then overdraw our bank account and cause tons of other issues too.

So my questions: Is this a known current issue with the IRS systems? It kind of looks like some sort of systems or data corruption problem on the IRS side. Second, what is the most expeditious way to resolve this? I think we will try to call the IRS tomorrow to see if we can get anywhere. Are there other things we should check, consider, and do?

As you might imagine, $100K missing is a bit of a shock at a minimum.

Thanks all in advance.

Edit: One added thing. We file jointly with me primary, and my wife as the spouse. However, my wife usually does all payments through her online account. This has for years never been a problem. Just wondering if we shouldn't do that or this could have contributed to this issue.