There is absolutely nothing wrong in this.
As per Section 31 tax invoice shall be issued before or at the time of removal of goods for supply to the recipient.
As per the rule 55(5), your client needs to issue the tax invoice for the complete quantity that is being moved in batches or lots.
Then he has to prepare the delivery challan for each batch/ lot and generate corresponding e-waybill for that batch/ lot and move the consignment with delivery challan, copy of invoice and e-waybill.
The last batch/ lot should have the original invoice along with delivery challan and e-waybill. On the e-waybill portal, he has to select "SKD/CKD/Lots" while generating e-waybill, with the delivery challan details.
However be prepared that field officers may/ may not be very conversant with all these provisions and hence, better to have the written correspondance with the supplier regarding the timing of invoice, delivery, lots etc handy in case goods are detained.