Have an issue with a check that was deleted out of the registry and such.

This is a semi complicated issues and I am seeking advice.  I have taken over my dad's business after his death and trying to get things all caught back up.

I am working on reconciling the checking account, which had not been done since like 2017 or 2018.  I have made it up to December of 2019 and ran into a glitch.

On the bank statement, I have a check that was generated and sent back to a customer.  We had to rework a part for them and they wanted their money back until the part was ready to ship again.  So the secretary that we had at the time created a credit memo and then used it to generate a refund check to send them, which we did.  

Now, for some unknown reason, said secretary (she has health issues that sometimes complicates her work) deleted the check out of the bank registry, and in turn, giving the customer back their credit on the credit memo.  Over time in 2020, said secretary used that credit memo for the customer on an order.  

If I go and add that check back into the registry (I know it's not in there as the check number does not exist in QB), it now jacks up their numbers on what they owe us and such.  I have attempted to work with them to collect these funds and they way they track their payments and such, is a pain to say the least and its been 2 years and I really don't want to fight about it.  I need to figure out how to place that check back into the registry with the correct dollar amount, so I can reconcile the bank account and then figure out how to remove the value from that customer, either as a bad debt or a journal entry or something, so their numbers reflect correctly.

Thank in advance guys.