IRS paid via check, funds not on clients account

I am at a loss on this one, hoping someone has run into it and resolved it. The client has assets with RBC bank, more of an investment account than a true 'bank'.

The client wrote a check to the IRS to settle an amended return balance and mailed it with the return. The IRS cashed the check, but now 8 months later sends a letter that the client owes the same amount.

Speaking to RBC and the IRS multiple times, RBC indicates that the IRS processed the check as an ACH, and therefore has no record of the canceled check front/back. IRS has no record of the payment on the client's account. There is an ACH confirmation I obtained from RBC, but none of those numbers was helpful to the two IRS agents I spoke to, and at least one of the agents was genuinely trying.

Best I can tell, the IRS keyed in the checking account/routing numbers and likely posted it to an incorrect SS#. But since I don't have the check, I cannot prove it. The IRS tried tracing the payment with the amended return that they acknowledge receiving, but that did not work.

Has anyone had a similar situation, and how did you resolve it?

I haven't had this happen, but the IRS should be able to put a tracer on it.
https://www.irs.gov/irm/part21/irm_21-005-007r

I did have this exact thing happen to a client recently. Same thing. Paper check was converted by the IRS to ACH about a year ago. A few weeks ago they get a notice saying they still owe the amount on the amended return. The agent tried all the numbers on the ACH receipt but couldn’t trace it. Client had to call the bank and get the tracer ID number. Once we had that, I called back again. They couldn’t find it still with that number but then suddenly the IRS agent said he could see the payment sitting in limbo on their account and hadn’t been applied to anything. So he was able to fix it. So just be persistent. I bet it’s there.

I think they’re having a lot of problems with amended returns. I have another amended return that was totally input incorrectly. Still trying to get that corrected. The agent can see it was input wrong but doesn’t have the power to fix it. Has to keep sending notes up to higher ups to reprocess it.