Did the employee's 5 days AWOL greatly affect the productivity of the Company that you would waste your time and effort for this?
The 30 days noticed is for the employee to turn over his work either 1) to his immediate superior or 2) to his replacements.Usually, during the 30 days period, the employee is the one who route his clearance so that any discrepancies can be addressed immediately. If this is the case, then considered the clearance put on hold, since the employee have failed to route the clearance.
If the HR is the one routing the clearance, then route it, so that you will know what liabilities the employee still have. If you put the clearance on hold, and there is a SENA, you cannot declare to the arbiter that the employee still have a liability since the clearance is put on hold.
The best thing you can do is whenever the employee ask for a certificate of employment, give him a CoE that his employment is until his AWOL date. Put in your records that he has been AWOL so that when a Background Check happens, you can state that he was AWOL. There is nothing wrong with stating what's on the record.