Say I placed an purchase order to my vendor 100pcs of stockable products at the price of 20.00 USD. 

After a month, I received 40 of them only because of material shortage.40pcs invoiced. Moreover the vendor claimed raw material cost rised a lot, they have to mark up 10% for the rest open items, that is 60 pcs * 22.00 = 1320.00 USD, and I have to wait 2 months to pick up.

Meanwhile, after receiving the first 40pcs, I delivered them to my customer. But I have to mark up 10% or 5% too in my open sale order line.

What is the best way to handle this case?

Thank you in advance.