SLA Exceptions

From Receivables module we have few activities shows incomplete in SLA due to either the trx_date being in closed period and accounted in current period etc.  Once the super users sees them didn't go through they book a manual journal, which leaves there transactions in sla and grows in SLA report..  Is there a way can we cleanup(cleanup script) these entries in SLA like flag them as processed if we know that it is booked in GL(with manual Journal).  What are all the best practices to handle these situations.  How do we fix the view accounting for these entries.