Load a new line for the additional 2 on the purchase order. You also need to load a credit note for the 2 you have returned from the purchase return and then apply it to the two you invoice on the original order. In correct processing your supplier should be creating a replacement order whilst processing the return, and this would naturally be a new order, but because they are not processing correctly you need to manipulate your end to reflect this.
Strangely you only have to think about “his” process if you want to - you are the “customer” so you are the one who should be looked after, so you should insist from an industry standard stand point that they process correctly, if they do not you have two choices, stop doing business with them, or alternatively bear the processing time, cost and errors of the credit memo approach - but that is YOUR decision to cope with the process the supplier is inflicting on YOU. In all honesty it is nothing to do with NAV - all systems will be in a similar position, once you receive the goods in and start processing and returning you are in a cycle of processing that is required to process through the paperwork and processes.