Hi,
It will be better if you cancel the excise invoice and reverse the other transaction also,
but as you have mention that due to some reason you cannot cancel the excise invoice, so one option is first you finish the complete cycle receiving the material in depot, and then again do the STO from Deport to manufacturing for same material with the same excise duties or do the return delivery from Depot to manufacturing plant.
Regards,
Zafar