Well if the item was sent out to a customer with doing a sales order, then your inventory is overstated and you would need to do a negative inventory adjustment to bring it back into balance. This way by doing the return you would increase it back to where it was before the mistake was made. You need to enter transactions as inventory items so your purchase receipts and IV HITB stay in agreement. You should hit the inventory and cogs GL accounts for both of these tranactions as this will net to zero.
I am not sure about your second part. In the first part you are saying the item was not on the invoice and then you are saying it was on the invoice. My gues is you should enter a new sales order to remove this item from inventory and now the stock quantity will be lower by whatever quantity was invoiced to the customer.