Help needed: I prepared a return where I did two amendments right afterwards and the tax payer received an notice with 97k payment request but should have gotten a refund of 10k

Im not a tax professional just a tax preparer.
Return was for mfj with two kids. I missed the overtime deduction on the original return so I filed amended return but didn’t realize that drake removed the direct deposit info so I did a superseded amendment to include dd info. All this was done on 02/01. Yesterday the received the notice and today we were able to reach irs after about 6 hours of holds and they are not able to see the amendments but will hold off on collections and further proceedings. They said to reply to the notice with all returns and submission ids via mail and they will review it.

Im open to all constructive and not so constructive criticism so I can learn from it.
Thanks in advance.