Ok
How often you get this scenario? SAP will ask you to reproduce this and I know you can't do that without knowing its reason. For cross check are you using any userexit etc for pricing in VF01? I hope you don't but just to make sure please check this.
Here I have a suggestion that why don't you change your process. Why users are deleting material from delivery? You need to check availability of material in order and if material is not there in stock system shouldn't confirm the stock and this unconfirmed stock will not be copied to delivery.
In delivery order you will not be deleting any line item and what you need to do is just PGI or enter batches if you have.
Thank$