Is it Islamically permissible for an accountant to settle the inventory by charging the deficit to the departments and removing the surplus from them, knowing that both the deficit and surplus result from the negligence of storekeepers, and that the company director is aware of this but has taken no action? And is this settlement considered as an approval of the theft that might occur because of it?

The physical inventory count for warehouses must be documented, and deficiencies should not be offset by surpluses. This is to review the reasons for shortages and surpluses and to hold accountable those who were negligent. This is unless the owner of the company or his representative agrees to settle the inventory in this manner. The approval of the company's manager is not sufficient unless he is authorized to do so.