The only problem I foresee is the Invoice date. It will be before the date of completion of supply. Also the chalan dates will be later than the Invoice dates.
One solution as suggested by my CA is to mention all the details like basic value, Taxes to be charged, consignment number, HSN code, GSTIN etc. in each chalan and attach a copy of the Purchase order received from the customer with each shipment. Issue a final Invoice with the last consignment. Do you think that is logical? more