Example would be if the PO is for 10, Receipted 10, but invoiced 12.

The order is still live, so you can use 'Write Off Incomplete Orders', but this only marks the header as complete and not the order lines.

I logged this with Sage Support as the only known issue (ID 7931) I could find relates to 'Free Text Items'  and the example I have relates to a stock item.

The response I got was 'R&D haven't documented a workaround to this particular side of the issue; but have instead suggested to use the Sage City Ideas Hub as a request for change. You could try amending the order in SQL directly, but this would be at your own testing with either demo or the customer's data offsite.'