Or I could modify the existing line item but the context is empty... The bill gets the line from the PO but the PO has $0 on the line because we don't know the cost of the service before it is complete and it's an intercompany transaction so we can't edit the PO to add the correct cost hence the vendor bill having $0 - the only time we can see the cost is when the invoice is entered into NS.

I dont think you can do swap an item and this is what will happen if you do it in NS UI. It will remove the link between the PO item and the Bill item if you change/swap the item on the bill. You can set the Bill item to $0.00 but hat will make the status of the bill Paid in Full.

You can't set an amount on an intercompany PO after it's been saved

I would create the PO only after the inter-co invoice, if applicable. If not, I don't think there's other way around using iterco transactions(I maybe wrong).

Yeah, I don't think their process can handle that because the other sub needs to link their SO to the PO and that has lots of other dependencies too