They eventually reply to letters.

If you are the third party designee you can call and 'splain.

"The IRS just sent them a notice that they owe $40,000 for 2020"

How do you know the issue is that one payment? Have them pull their tax account transcript:

https://www.irs.gov/individuals/get-transcript

Was the check for $40,000?

Did they mail it with a 1040-ES voucher for 2020?

They eventually respond to letters.  You can call and listen to music for three hours and someone will tell you to mail them a copy of the front and back of the check.  Or you can do that without calling.  

Respond to the letter with copies of the canceled check that they arent showing record of receiving.