Expenditure Transaction causing discrepancy between Project Balances & Control Budget Balances

We have unapproved fund status expenditure transaction causing discrepancy between Project Balances and Control Budget Balances. The expenditure transaction is accounted in Project Balances but not in Control Budget Balances. It shows the expenditure transaction (miscellaneous transaction) cannot be cancelled since it is already fully AR invoiced. We are looking for inputs and suggestion how we can resolve this discrepancy and allow the user to submit requisition based on the correct funds available.