Hi Ian,
This has been a problem for us also and we are trying hard to find out a solution for this but in vain.
The best possible way for this to do the transaction is as follows.
1. For the entire main component, do the returns and do PGR.
2. Once this is done, Create another outbound delivery for this main component, but this time remove the BOM component which is returned. This should set the transaction right.
However if you are controlling cost in accurate way through SAP and if you use moving average, then it will have impact in material costing and MM and CO team should ratify this solution. This is exactly where we have problem. We are very specific about costing implications as we handle costs per project. Dont know about your situation. If the solution suits you, you can adopt this.