PO from work order, allocation vs change in finished goods quantity

I'm hoping someone can assist in this scenario and what the proper procedure should be:

we create a work order for 40000 kg of finished product

allocation of raw material is done

PO is created from work order which is sent to toller

now material is reworked however the quantity is less - example 32940. kgs.

have found that the work order displays an additional line in the operations for the balance, 7060kgs. in addition see that my allocated material required have changed.

We manually allocate the raw material and do not want this to change.   In addition, would we need to manually exclude the balance on the operations line since we are not receiving the full 40000 kgs and want to complete it as 32940?   

I need to have a process in place to train other users but I'm not sure what the proper course of action would be if the finished goods is more or less what is entered.

any help appreciated- thanks

c