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I have noticed similar situation in a mfg company, let me give a brief idea on the same to see if it helps:
1.) They try to detach the freight piece from the actual PO.
2.) They raise new POs for the freight alone, using PDOI programs.
3.) These are kicked off by the receipt/partial receipt, a custom conc program looks at the original PO (against which the goods is received), it copies the supplier etc.. on to a new PO.
4.) Amount is derived carefully everytime. Status of the PO can be calculated/controlled.
5.) Appropriate line types are used for Freight.
In your scenario, this might result in 2 invoices for one PO.
For 1000 => you do a 500 in invoice-1 then 500 in invoice-2 both against the new PO (original PO is safely approved and closed/finally closed)
You might need to look at the feasibility at greater depths.
All the best !!
Other option is to use Complex Work Procurement.. (Plus some customizations)