We have two similar problems we don't know how to solve.
First, we made a deposit of 10 checks. The bank recorded the total and we were able to reconcile. But then, we got a note saying of the checks was missing and we have an entry from the bank that takes the 12.36 out of our bank account. We have no idea where to charge it to.
Second, we make a deposit and mistakenly recorded the total payment of $1500 when the check was partial payment of $250. Again, we were able to reconcile the bank deposit, but now, we have a charge back of $1250 we don't know what to do with.